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kraken2: fix linter and remove unpaired paired input #7062

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kraken2: fix linter and remove unpaired paired input #7062

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2 changes: 0 additions & 2 deletions tool_collections/kraken2/kraken2/.lint_skip
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80 changes: 28 additions & 52 deletions tool_collections/kraken2/kraken2/kraken2.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy1">
<tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy2">
<description>
assign taxonomic labels to sequencing reads
</description>
Expand Down Expand Up @@ -40,10 +40,7 @@

$quick

#if $single_paired.single_paired_selector == "yes"
--paired
'${single_paired.forward_input}' '${single_paired.reverse_input}'
#elif $single_paired.single_paired_selector == "collection":
#if $single_paired.single_paired_selector == "collection":
--paired
'${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
#else:
Expand Down Expand Up @@ -80,17 +77,12 @@
<inputs>
<conditional name="single_paired">
<param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
<option value="collection">Paired Collection</option>
<option value="yes">Paired</option>
<option value="collection">Paired</option>
<option selected="True" value="no">Single</option>
</param>
<when value="collection">
<param format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/>
</when>
<when value="yes">
<param format="@INTYPES@" name="forward_input" type="data" label="Forward strand"/>
<param format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand"/>
</when>
<when value="no">
<param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data"/>
</when>
Expand Down Expand Up @@ -122,19 +114,6 @@
<filter>(report['create_report'])</filter>
</data>

<data name="out1" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified forward reads" from_work_dir="un_out_1.*">
<filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
</data>
<data name="out2" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified reverse reads" from_work_dir="un_out_2.*">
<filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
</data>
<data name="out3" format_source="forward_input" label="${tool.name} on ${on_string}: Classified forward reads" from_work_dir="cl_out_1.*">
<filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
</data>
<data name="out4" format_source="forward_input" label="${tool.name} on ${on_string}: Classified reverse reads" from_work_dir="cl_out_2.*">
<filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
</data>

<collection name="out_unclassified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Unclassified read pairs">
<data name="forward" from_work_dir="un_out_1.*"/>
<data name="reverse" from_work_dir="un_out_2.*"/>
Expand All @@ -151,37 +130,27 @@
</outputs>
<tests>
<test expect_num_outputs="1">
<param name="single_paired_selector" value="no"/>
<param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
<conditional name="single_paired">
<param name="single_paired_selector" value="no"/>
<param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
</conditional>
<param name="split_reads" value="false"/>
<param name="quick" value="no"/>
<param name="confidence" value=".2"/>
<param name="kraken2_database" value="test_entry"/>
<output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
</test>
<test expect_num_outputs="5">
<param name="single_paired_selector" value="yes"/>
<param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/>
<param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/>
<param name="split_reads" value="true"/>
<param name="quick" value="no"/>
<param name="confidence" value="0"/>
<param name="kraken2_database" value="test_entry"/>
<output name="out1" file="un_test2_output_1.fastq" ftype="fastq"/>
<output name="out2" file="un_test2_output_2.fastq" ftype="fastq"/>
<output name="out3" file="cl_test2_output_1.fastq" ftype="fastq"/>
<output name="out4" file="cl_test2_output_2.fastq" ftype="fastq"/>
<output name="output" file="kraken_test2_output.tab" ftype="tabular"/>
</test>
<!-- same test but collection in/output -->
<test expect_num_outputs="7">
<param name="single_paired_selector" value="collection"/>
<param name="input_pair">
<collection type="paired">
<element name="forward" value="kraken_test2_R1.fastq" ftype="fastq"/>
<element name="reverse" value="kraken_test2_R2.fastq" ftype="fastq"/>
</collection>
</param>
<conditional name="single_paired">
<param name="single_paired_selector" value="collection"/>
<param name="input_pair">
<collection type="paired">
<element name="forward" value="kraken_test2_R1.fastq" ftype="fastq"/>
<element name="reverse" value="kraken_test2_R2.fastq" ftype="fastq"/>
</collection>
</param>
<param name="single_paired_selector" value="collection"/>
</conditional>
<param name="split_reads" value="true"/>
<param name="quick" value="no"/>
<param name="confidence" value="0"/>
Expand All @@ -196,11 +165,18 @@
</output_collection>
<output name="output" file="kraken_test2_output.tab" ftype="tabular"/>
</test>

<test expect_num_outputs="2">
<param name="single_paired_selector" value="yes"/>
<param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/>
<param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/>
<param name="use-names" value="true"/>
<conditional name="single_paired">
<param name="single_paired_selector" value="collection"/>
<param name="input_pair">
<collection type="paired">
<element name="forward" value="kraken_test2_R1.fastq" ftype="fastq"/>
<element name="reverse" value="kraken_test2_R2.fastq" ftype="fastq"/>
</collection>
</param>
</conditional>
<param name="use_names" value="true"/>
<section name="report">
<param name="create_report" value="true"/>
<param name="report_minimizer_data" value="true"/>
Expand Down
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