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mr-cmr-c
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Support draft-3 long form input arrays
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4 files changed

+659
-11
lines changed

4 files changed

+659
-11
lines changed

‎cwlupgrader/main.py

Lines changed: 12 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -586,18 +586,20 @@ def input_output_clean(document: Dict[str, Any]) -> None:
586586
if "$import" in param:
587587
meta = True
588588
if not meta:
589-
for index2, param in enumerate(document[param_type]):
589+
for index2, param2 in enumerate(document[param_type]):
590590
with SourceLine(document[param_type], index2, Exception):
591-
param_id = param.pop("id").lstrip("#")
592-
if "type" in param:
593-
param["type"] = shorten_type(param["type"])
594-
array_type_raise_sf(param)
595-
if "description" in param:
596-
param["doc"] = param.pop("description")
597-
if len(param) > 1:
598-
new_section[param_id] = sort_input_or_output(param)
591+
param_id = param2.pop("id").lstrip("#")
592+
if "type" in param2:
593+
param2["type"] = shorten_type(param2["type"])
594+
array_type_raise_sf(param2)
595+
if "description" in param2:
596+
param2["doc"] = param2.pop("description")
597+
if len(param2) > 1:
598+
new_section[param_id] = sort_input_or_output(param2)
599+
elif "type" in param2 and isinstance(param2["type"], str):
600+
new_section[param_id] = param2.popitem()[1]
599601
else:
600-
new_section[param_id] = param.popitem()[1]
602+
new_section[param_id] = param2
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document[param_type] = new_section
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603605

‎testdata/draft-3/attributor-prok-cheetah.cwl

Lines changed: 328 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,328 @@
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#!/usr/bin/env cwl-runner
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# Source: https://github.com/jorvis/GALES/blob/cc869204cdb004a7c952900692a97b4edd228e6d/cwl/tools/attributor-prok-cheetah.cwl
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# Copyright (c) 2016 Joshua Orvis
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#
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# Permission is hereby granted, free of charge, to any person obtaining a copy
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# of this software and associated documentation files (the "Software"), to deal
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# in the Software without restriction, including without limitation the rights
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# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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# copies of the Software, and to permit persons to whom the Software is
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# furnished to do so, subject to the following conditions:
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#
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# The above copyright notice and this permission notice shall be included in all
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# copies or substantial portions of the Software.
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#
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# SOFTWARE.
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cwlVersion: "cwl:draft-3"
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class: CommandLineTool
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baseCommand: attributor
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requirements:
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- class: InlineJavascriptRequirement
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- class: CreateFileRequirement
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fileDef:
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- filename: attributor.config
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fileContent: |
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general:
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default_product_name: hypothetical protein
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allow_attributes_from_multiple_sources: No
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debugging_polypeptide_limit: 0
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indexes:
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coding_hmm_lib: $(inputs.hmm_attribute_lookup_file.path)
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uniref100: $(inputs.blast_attribute_lookup_file.path)
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input:
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polypeptide_fasta: $(inputs.polypeptide_fasta.path)
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gff3: $(inputs.source_gff3.path)
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order:
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- coding_hmm_lib__equivalog
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- rapsearch2__trusted_full_full
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- coding_hmm_lib__equivalog_domain
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- rapsearch2__trusted_partial_full
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- coding_hmm_lib__subfamily
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- coding_hmm_lib__superfamily
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- coding_hmm_lib__subfamily_domain
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- coding_hmm_lib__domain
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- coding_hmm_lib__pfam
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- rapsearch2__trusted_full_partial
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- rapsearch2__all_full_full
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- tmhmm
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#- lipoprotein_motif
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- coding_hmm_lib__hypothetical_equivalog
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evidence:
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- label: coding_hmm_lib__equivalog
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type: HMMer3_htab
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path: ${
64+
var r = "";
65+
for (var i = 0; i < inputs.hmm_files.length; i++) {
66+
if (i > 0) {
67+
r += ",";
68+
}
69+
r += inputs.hmm_files[i].path.replace('file://','');
70+
}
71+
return r;
72+
}
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class: equivalog
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index: coding_hmm_lib
75+
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- label: coding_hmm_lib__equivalog_domain
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type: HMMer3_htab
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path: ${
79+
var r = "";
80+
for (var i = 0; i < inputs.hmm_files.length; i++) {
81+
if (i > 0) {
82+
r += ",";
83+
}
84+
r += inputs.hmm_files[i].path.replace('file://','');
85+
}
86+
return r;
87+
}
88+
class: equivalog_domain
89+
index: coding_hmm_lib
90+
91+
- label: coding_hmm_lib__subfamily
92+
type: HMMer3_htab
93+
path: ${
94+
var r = "";
95+
for (var i = 0; i < inputs.hmm_files.length; i++) {
96+
if (i > 0) {
97+
r += ",";
98+
}
99+
r += inputs.hmm_files[i].path.replace('file://','');
100+
}
101+
return r;
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}
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class: subfamily
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index: coding_hmm_lib
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append_text: family protein
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- label: coding_hmm_lib__superfamily
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type: HMMer3_htab
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path: ${
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var r = "";
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for (var i = 0; i < inputs.hmm_files.length; i++) {
112+
if (i > 0) {
113+
r += ",";
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}
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r += inputs.hmm_files[i].path.replace('file://','');
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}
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return r;
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}
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class: superfamily
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index: coding_hmm_lib
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append_text: family protein
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- label: coding_hmm_lib__subfamily_domain
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type: HMMer3_htab
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path: ${
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var r = "";
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for (var i = 0; i < inputs.hmm_files.length; i++) {
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if (i > 0) {
129+
r += ",";
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}
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r += inputs.hmm_files[i].path.replace('file://','');
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}
133+
return r;
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}
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class: subfamily_domain
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index: coding_hmm_lib
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append_text: domain protein
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- label: coding_hmm_lib__domain
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type: HMMer3_htab
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path: ${
142+
var r = "";
143+
for (var i = 0; i < inputs.hmm_files.length; i++) {
144+
if (i > 0) {
145+
r += ",";
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}
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r += inputs.hmm_files[i].path.replace('file://','');
148+
}
149+
return r;
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}
151+
class: domain
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index: coding_hmm_lib
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append_text: domain protein
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- label: coding_hmm_lib__pfam
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type: HMMer3_htab
157+
path: ${
158+
var r = "";
159+
for (var i = 0; i < inputs.hmm_files.length; i++) {
160+
if (i > 0) {
161+
r += ",";
162+
}
163+
r += inputs.hmm_files[i].path.replace('file://','');
164+
}
165+
return r;
166+
}
167+
class: pfam
168+
index: coding_hmm_lib
169+
append_text: family protein
170+
171+
- label: coding_hmm_lib__hypothetical_equivalog
172+
type: HMMer3_htab
173+
path: ${
174+
var r = "";
175+
for (var i = 0; i < inputs.hmm_files.length; i++) {
176+
if (i > 0) {
177+
r += ",";
178+
}
179+
r += inputs.hmm_files[i].path.replace('file://','');
180+
}
181+
return r;
182+
}
183+
class: hypoth_equivalog
184+
index: coding_hmm_lib
185+
186+
- label: rapsearch2__trusted_full_full
187+
type: RAPSearch2_m8
188+
path: ${
189+
var r = "";
190+
for (var i = 0; i < inputs.m8_files.length; i++) {
191+
if (i > 0) {
192+
r += ",";
193+
}
194+
r += inputs.m8_files[i].path.replace('file://','');
195+
}
196+
return r;
197+
}
198+
class: trusted
199+
index: uniref100
200+
query_cov: 80%
201+
match_cov: 80%
202+
percent_identity_cutoff: 50%
203+
204+
- label: rapsearch2__trusted_partial_full
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type: RAPSearch2_m8
206+
path: ${
207+
var r = "";
208+
for (var i = 0; i < inputs.m8_files.length; i++) {
209+
if (i > 0) {
210+
r += ",";
211+
}
212+
r += inputs.m8_files[i].path.replace('file://','');
213+
}
214+
return r;
215+
}
216+
class: trusted
217+
index: uniref100
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match_cov: 80%
219+
percent_identity_cutoff: 50%
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append_text: domain protein
221+
222+
- label: rapsearch2__trusted_full_partial
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type: RAPSearch2_m8
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path: ${
225+
var r = "";
226+
for (var i = 0; i < inputs.m8_files.length; i++) {
227+
if (i > 0) {
228+
r += ",";
229+
}
230+
r += inputs.m8_files[i].path.replace('file://','');
231+
}
232+
return r;
233+
}
234+
class: trusted
235+
index: uniref100
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query_cov: 80%
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percent_identity_cutoff: 50%
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append_text: domain protein
239+
240+
- label: rapsearch2__all_full_full
241+
type: RAPSearch2_m8
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path: ${
243+
var r = "";
244+
for (var i = 0; i < inputs.m8_files.length; i++) {
245+
if (i > 0) {
246+
r += ",";
247+
}
248+
r += inputs.m8_files[i].path.replace('file://','');
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}
250+
return r;
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}
252+
index: uniref100
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query_cov: 80%
254+
match_cov: 80%
255+
percent_identity_cutoff: 50%
256+
prepend_text: putative
257+
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- label: tmhmm
259+
type: TMHMM
260+
product_name: putative integral membrane protein
261+
min_helical_spans: 5
262+
path: ${
263+
var r = "";
264+
for (var i = 0; i < inputs.tmhmm_files.length; i++) {
265+
if (i > 0) {
266+
r += ",";
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}
268+
r += inputs.tmhmm_files[i].path.replace('file://','');
269+
}
270+
return r;
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}
272+
273+
hints:
274+
- class: DockerRequirement
275+
dockerPull: jorvis/gales-gce
276+
277+
inputs:
278+
- id: config_file
279+
type: string
280+
inputBinding:
281+
prefix: -c
282+
separate: true
283+
position: 1
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- id: output_base
285+
type: string
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inputBinding:
287+
position: 2
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prefix: -o
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separate: true
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- id: output_format
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type: string
292+
inputBinding:
293+
position: 3
294+
prefix: -f
295+
separate: true
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- id: hmm_attribute_lookup_file
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type: File
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- id: blast_attribute_lookup_file
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type: File
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- id: polypeptide_fasta
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type: File
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- id: source_gff3
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type: File
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- id: hmm_files
305+
type:
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type: array
307+
items: File
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- id: m8_files
309+
type:
310+
type: array
311+
items: File
312+
- id: tmhmm_files
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type:
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type: array
315+
items: File
316+
317+
318+
outputs:
319+
- id: output_files
320+
type:
321+
type: array
322+
items: File
323+
outputBinding:
324+
glob: $(inputs.output_base + '*')
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- id: the_config
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type: File
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outputBinding:
328+
glob: 'attributor.config'

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