Update sequence util (#7483)

* fix #5333

disallow fastq input will lead to a wrong value of the CLI parameter
`'${input_file.extension[len('fastq'):]}'`

* fastq filter: fix tests

* fastq groomer: fix tests

* fastq manipulation: fix tests

* fastq paired interlacer: fix tests and adapt output labels

* fastq trimmer: fix tests

* bump

* produce paired collections

* fix py2 error

* manually bump one tool

Author: bernt-matthias

tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip

@@ -109,12 +109,16 @@ def fastq_read_pass_filter(fastq_read):
             <param name="max_quality" value="0"/>
             <param name="max_num_deviants" value="0"/>
             <param name="paired_end" value="false"/>
-            <param name="base_offset_type" value="offsets_absolute"/>
-            <param name="left_column_offset" value="0"/>
-            <param name="right_column_offset" value="0"/>
-            <param name="score_operation" value="min"/>
-            <param name="score_comparison" value="&gt;="/>
-            <param name="score" value="0"/>
+            <repeat name="fastq_filters">
+                <conditional name="offset_type">
+                    <param name="base_offset_type" value="offsets_absolute"/>
+                    <param name="left_column_offset" value="0"/>
+                    <param name="right_column_offset" value="0"/>
+                </conditional>
+                <param name="score_operation" value="min"/>
+                <param name="score_comparison" value="&gt;="/>
+                <param name="score" value="0"/>
+            </repeat>
             <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
         </test>
         <!-- Do nothing filter compressed -->
@@ -126,12 +130,16 @@ def fastq_read_pass_filter(fastq_read):
             <param name="max_quality" value="0"/>
             <param name="max_num_deviants" value="0"/>
             <param name="paired_end" value="false"/>
-            <param name="base_offset_type" value="offsets_absolute"/>
-            <param name="left_column_offset" value="0"/>
-            <param name="right_column_offset" value="0"/>
-            <param name="score_operation" value="min"/>
-            <param name="score_comparison" value="&gt;="/>
-            <param name="score" value="0"/>
+            <repeat name="fastq_filters">
+                <conditional name="offset_type">
+                    <param name="base_offset_type" value="offsets_absolute"/>
+                    <param name="left_column_offset" value="0"/>
+                    <param name="right_column_offset" value="0"/>
+                </conditional>
+                <param name="score_operation" value="min"/>
+                <param name="score_comparison" value="&gt;="/>
+                <param name="score" value="0"/>
+            </repeat>
             <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastqsanger.gz" decompress="true"/>
         </test>
         <!-- crippled input types prevent this test <test>
@@ -159,12 +167,16 @@ def fastq_read_pass_filter(fastq_read):
             <param name="max_quality" value="0"/>
             <param name="max_num_deviants" value="0"/>
             <param name="paired_end" value="false"/>
-            <param name="base_offset_type" value="offsets_absolute"/>
-            <param name="left_column_offset" value="0"/>
-            <param name="right_column_offset" value="0"/>
-            <param name="score_operation" value="min"/>
-            <param name="score_comparison" value="&gt;="/>
-            <param name="score" value="0"/>
+            <repeat name="fastq_filters">
+                <conditional name="offset_type">
+                    <param name="base_offset_type" value="offsets_absolute"/>
+                    <param name="left_column_offset" value="0"/>
+                    <param name="right_column_offset" value="0"/>
+                </conditional>
+                <param name="score_operation" value="min"/>
+                <param name="score_comparison" value="&gt;="/>
+                <param name="score" value="0"/>
+            </repeat>
             <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
         </test>
         <!-- Remove all Filter -->
@@ -176,12 +188,16 @@ def fastq_read_pass_filter(fastq_read):
             <param name="max_quality" value="0"/>
             <param name="max_num_deviants" value="0"/>
             <param name="paired_end" value="false"/>
-            <param name="base_offset_type" value="offsets_absolute"/>
-            <param name="left_column_offset" value="0"/>
-            <param name="right_column_offset" value="0"/>
-            <param name="score_operation" value="min"/>
-            <param name="score_comparison" value="&gt;="/>
-            <param name="score" value="0"/>
+            <repeat name="fastq_filters">
+                <conditional name="offset_type">
+                    <param name="base_offset_type" value="offsets_absolute"/>
+                    <param name="left_column_offset" value="0"/>
+                    <param name="right_column_offset" value="0"/>
+                </conditional>
+                <param name="score_operation" value="min"/>
+                <param name="score_comparison" value="&gt;="/>
+                <param name="score" value="0"/>
+            </repeat>
             <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
         </test>
         <!-- crippled input types prevent this test <test>
@@ -209,12 +225,16 @@ def fastq_read_pass_filter(fastq_read):
             <param name="max_quality" value="0"/>
             <param name="max_num_deviants" value="1"/>
             <param name="paired_end" value="false"/>
-            <param name="base_offset_type" value="offsets_absolute"/>
-            <param name="left_column_offset" value="0"/>
-            <param name="right_column_offset" value="0"/>
-            <param name="score_operation" value="min"/>
-            <param name="score_comparison" value="&gt;="/>
-            <param name="score" value="0"/>
+            <repeat name="fastq_filters">
+                <conditional name="offset_type">
+                    <param name="base_offset_type" value="offsets_absolute"/>
+                    <param name="left_column_offset" value="0"/>
+                    <param name="right_column_offset" value="0"/>
+                </conditional>
+                <param name="score_operation" value="min"/>
+                <param name="score_comparison" value="&gt;="/>
+                <param name="score" value="0"/>
+            </repeat>
             <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
         </test>
         <!-- crippled input types prevent this test<test>
@@ -242,12 +262,16 @@ def fastq_read_pass_filter(fastq_read):
             <param name="max_quality" value="0"/>
             <param name="max_num_deviants" value="0"/>
             <param name="paired_end" value="false"/>
-            <param name="base_offset_type" value="offsets_absolute"/>
-            <param name="left_column_offset" value="1"/>
-            <param name="right_column_offset" value="1"/>
-            <param name="score_operation" value="min"/>
-            <param name="score_comparison" value="&gt;="/>
-            <param name="score" value="1"/>
+            <repeat name="fastq_filters">
+                <conditional name="offset_type">
+                    <param name="base_offset_type" value="offsets_absolute"/>
+                    <param name="left_column_offset" value="1"/>
+                    <param name="right_column_offset" value="1"/>
+                </conditional>
+                <param name="score_operation" value="min"/>
+                <param name="score_comparison" value="&gt;="/>
+                <param name="score" value="1"/>
+            </repeat>
             <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
         </test>
         <test>
@@ -258,12 +282,16 @@ def fastq_read_pass_filter(fastq_read):
             <param name="max_quality" value="0"/>
             <param name="max_num_deviants" value="0"/>
             <param name="paired_end" value="false"/>
-            <param name="base_offset_type" value="offsets_absolute"/>
-            <param name="left_column_offset" value="1"/>
-            <param name="right_column_offset" value="1"/>
-            <param name="score_operation" value="max"/>
-            <param name="score_comparison" value="&lt;="/>
-            <param name="score" value="92"/>
+            <repeat name="fastq_filters">
+                <conditional name="offset_type">
+                    <param name="base_offset_type" value="offsets_absolute"/>
+                    <param name="left_column_offset" value="1"/>
+                    <param name="right_column_offset" value="1"/>
+                </conditional>
+                <param name="score_operation" value="max"/>
+                <param name="score_comparison" value="&lt;="/>
+                <param name="score" value="92"/>
+            </repeat>
             <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
         </test>
         <!-- percent based offsets -->
@@ -275,12 +303,16 @@ def fastq_read_pass_filter(fastq_read):
             <param name="max_quality" value="0"/>
             <param name="max_num_deviants" value="0"/>
             <param name="paired_end" value="false"/>
-            <param name="base_offset_type" value="offsets_percent"/>
-            <param name="left_column_offset" value="1.075"/>
-            <param name="right_column_offset" value="1.075"/>
-            <param name="score_operation" value="min"/>
-            <param name="score_comparison" value="&gt;="/>
-            <param name="score" value="1"/>
+            <repeat name="fastq_filters">
+                <conditional name="offset_type">
+                    <param name="base_offset_type" value="offsets_percent"/>
+                    <param name="left_column_offset" value="1.075"/>
+                    <param name="right_column_offset" value="1.075"/>
+                </conditional>
+                <param name="score_operation" value="min"/>
+                <param name="score_comparison" value="&gt;="/>
+                <param name="score" value="1"/>
+            </repeat>
             <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
         </test>
         <test>
@@ -291,12 +323,16 @@ def fastq_read_pass_filter(fastq_read):
             <param name="max_quality" value="0"/>
             <param name="max_num_deviants" value="0"/>
             <param name="paired_end" value="true"/>
-            <param name="base_offset_type" value="offsets_percent"/>
-            <param name="left_column_offset" value="1"/>
-            <param name="right_column_offset" value="1"/>
-            <param name="score_operation" value="min"/>
-            <param name="score_comparison" value="&gt;="/>
-            <param name="score" value="1"/>
+            <repeat name="fastq_filters">
+                <conditional name="offset_type">
+                    <param name="base_offset_type" value="offsets_percent"/>
+                    <param name="left_column_offset" value="1"/>
+                    <param name="right_column_offset" value="1"/>
+                </conditional>
+                <param name="score_operation" value="min"/>
+                <param name="score_comparison" value="&gt;="/>
+                <param name="score" value="1"/>
+            </repeat>
             <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
         </test>
     </tests>