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Merge pull request #6360 from bernt-matthias/lint-iedb_api
Fix linter errors for iedb api
2 parents f78b4c5 + 6e91dab commit 69cdfd8

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-14
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+35
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‎tools/iedb_api/.lint_skip‎

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‎tools/iedb_api/iedb_api.xml‎

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Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
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<description>MHC Binding prediction</description>
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<macros>
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<token name="@TOOL_VERSION@">2.15.3</token>
5-
<token name="@VERSION_SUFFIX@">0</token>
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<token name="@VERSION_SUFFIX@">1</token>
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<token name="@PROFILE@">24.2</token>
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<xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples="">
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<conditional name="alleles">
@@ -108,7 +108,7 @@ $seqtext
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<option value="netmhccons">netmhccons</option>
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<option value="pickpocket">pickpocket</option>
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</param>
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<expand macro="alleles" hla_regex="(HLA-[A-CEG]\*[0-8][[0-9]:[0-9][0-9][0-9]*|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-5]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/>
111+
<expand macro="alleles" hla_regex="(HLA-[A-CEG]\*[0-8][0-9]:[0-9][0-9][0-9]*|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-5]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/>
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<param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
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<help>Used for any alleles which don't include specified lengths</help>
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<option value="8" selected="true">8</option>
@@ -172,7 +172,7 @@ $seqtext
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<option value="immuno">immuno</option>
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<option value="constitutive">constitutive</option>
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</param>
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<expand macro="alleles" hla_regex="(HLA-[A-CE]\*[0-8][[0-9]:[0-9][0-9]|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-4]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/>
175+
<expand macro="alleles" hla_regex="(HLA-[A-CE]\*[0-8][0-9]:[0-9][0-9]|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-4]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/>
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<param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
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<help>Used for any alleles which don't include specified lengths</help>
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<option value="8" selected="true">8</option>
@@ -236,12 +236,12 @@ $seqtext
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-->
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<data name="output" format="tabular" label="IEDB ${prediction.tool} ${prediction.method}"/>
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<data name="output2" format="tabular" label="IEDB ${prediction.tool} ${prediction.method} residue scores" from_work_dir="iedb_results2">
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<filter>prediction['method'].startswith('Bepipred')</filter>
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<filter>prediction['method'] == 'Bepipred'</filter>
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</data>
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</outputs>
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<tests>
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<!-- test1 -->
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<test>
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<test expect_num_outputs="1">
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<conditional name="prediction">
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<param name="tool" value="mhci"/>
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<param name="method" value="recommended"/>
@@ -261,7 +261,7 @@ $seqtext
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</output>
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</test>
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<!-- test2 -->
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<test>
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<test expect_num_outputs="1">
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<conditional name="prediction">
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<param name="tool" value="mhci"/>
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<param name="method" value="recommended"/>
@@ -282,7 +282,7 @@ $seqtext
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</output>
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</test>
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<!-- test3 -->
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<test>
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<test expect_num_outputs="1">
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<conditional name="prediction">
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<param name="tool" value="mhci"/>
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<param name="method" value="recommended"/>
@@ -306,7 +306,7 @@ $seqtext
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</output>
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</test>
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<!-- test4 -->
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<test>
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<test expect_num_outputs="1">
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<conditional name="prediction">
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<param name="tool" value="mhcii"/>
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<param name="method" value="recommended"/>
@@ -327,7 +327,7 @@ $seqtext
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</output>
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</test>
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<!-- test5 -->
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<test>
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<test expect_num_outputs="1">
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<conditional name="prediction">
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<param name="tool" value="processing"/>
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<param name="method" value="recommended"/>
@@ -348,7 +348,7 @@ $seqtext
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</output>
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</test>
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<!-- test6 -->
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<test>
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<test expect_num_outputs="1">
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<conditional name="prediction">
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<param name="tool" value="mhcnp"/>
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<param name="method" value="mhcnp"/>
@@ -368,7 +368,7 @@ $seqtext
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</output>
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</test>
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<!-- test7 -->
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<test>
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<test expect_num_outputs="1">
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<conditional name="prediction">
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<param name="tool" value="bcell"/>
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<param name="method" value="Emini"/>
@@ -384,7 +384,7 @@ $seqtext
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</output>
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</test>
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<!-- test8 -->
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<test>
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<test expect_num_outputs="1">
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<conditional name="prediction">
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<param name="tool" value="bcell"/>
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<param name="method" value="Kolaskar-Tongaonkar"/>
@@ -400,6 +400,29 @@ $seqtext
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</assert_contents>
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</output>
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</test>
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<!-- test9 test 2nd output for Bepipred, no idea if its possible to have output non-empty -->
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<test expect_num_outputs="2">
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<conditional name="prediction">
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<param name="tool" value="bcell"/>
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<param name="method" value="Bepipred"/>
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<param name="window_size" value="9"/>
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</conditional>
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<conditional name="sequence">
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<param name="seqsrc" value="fasta"/>
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<param name="seq_fasta" ftype="fasta" value="bcell.fa"/>
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</conditional>
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<output name="output">
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<assert_contents>
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<has_n_lines n="0" />
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</assert_contents>
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</output>
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<output name="output2">
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<assert_contents>
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<has_n_lines n="106"/>
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<has_n_columns n="5"/>
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</assert_contents>
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</output>
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</test>
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</tests>
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<help><![CDATA[

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