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fix linting errors: disco #6354

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fix linting errors: disco #6354

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3 changes: 0 additions & 3 deletions tools/disco/.lint_skip
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Original file line number Diff line number Diff line change
@@ -1,4 +1 @@
CitationsNoValid
InputsNameDuplicateOutput
TestsExpectNumOutputs
XMLOrder
20 changes: 10 additions & 10 deletions tools/disco/disco.xml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,5 @@
<tool id="disco" name="DISCO" version="@WRAPPER_VERSION@.1" profile="20.01">
<tool id="disco" name="DISCO" version="@WRAPPER_VERSION@.2" profile="20.01">
<description>to assemble metagenomics data using an overlap-layout-consensus (OLC) approach</description>
<xrefs>
<xref type="bio.tools">disco</xref>
</xrefs>
<macros>
<token name="@WRAPPER_VERSION@">1.2</token>
<xml name="assembly_params">
Expand All @@ -20,6 +17,9 @@
<param argument="minEdgeLengthToBe1MinFlow" type="integer" value="2000" min="0" label="Minimum edge length to be assigned with 1 minimum flow"/>
</xml>
</macros>
<xrefs>
<xref type="bio.tools">disco</xref>
</xrefs>
<requirements>
<requirement type="package" version="@WRAPPER_VERSION@">disco</requirement>
</requirements>
Expand Down Expand Up @@ -189,7 +189,7 @@ minEdgeLengthToBe1MinFlow = $third_assembly_iter_param.minEdgeLengthToBe1MinFlow
</section>
</inputs>
<outputs>
<data format="txt" name="log" from_work_dir="disco.log" label="${tool.name} on ${on_string}: Log file">
<data format="txt" name="log_out" from_work_dir="disco.log" label="${tool.name} on ${on_string}: Log file">
<filter>log</filter>
</data>
<data format="fasta" name="contigs" from_work_dir="disco_contigsFinalCombined.fasta" label="${tool.name} on ${on_string}: Contigs"/>
Expand All @@ -208,7 +208,7 @@ minEdgeLengthToBe1MinFlow = $third_assembly_iter_param.minEdgeLengthToBe1MinFlow
</collection>
</outputs>
<tests>
<test>
<test expect_num_outputs="6">
<conditional name="input_cond">
<param name="library_type" value="paired"/>
<conditional name="paired_input">
Expand Down Expand Up @@ -266,7 +266,7 @@ minEdgeLengthToBe1MinFlow = $third_assembly_iter_param.minEdgeLengthToBe1MinFlow
<param name="minReadsCountInEdgeToBe1MinFlow" value="20"/>
<param name="minEdgeLengthToBe1MinFlow" value="2000"/>
</section>
<output name="log">
<output name="log_out">
<assert_contents>
<has_text text="Software: Disco Assembler" />
<has_text text="FIRST LOOP ITERATION 1" />
Expand Down Expand Up @@ -301,7 +301,7 @@ minEdgeLengthToBe1MinFlow = $third_assembly_iter_param.minEdgeLengthToBe1MinFlow
<element name="1" file="test1_graph_1.gfa2" compare="sim_size" delta="6000"/>
</output_collection>
</test>
<test>
<test expect_num_outputs="3">
<conditional name="input_cond">
<param name="library_type" value="paired"/>
<conditional name="paired_input">
Expand Down Expand Up @@ -358,7 +358,7 @@ minEdgeLengthToBe1MinFlow = $third_assembly_iter_param.minEdgeLengthToBe1MinFlow
<param name="minReadsCountInEdgeToBe1MinFlow" value="20"/>
<param name="minEdgeLengthToBe1MinFlow" value="2000"/>
</section>
<output name="log">
<output name="log_out">
<assert_contents>
<has_text text="Software: Disco Assembler" />
<has_text text="FIRST LOOP ITERATION 1" />
Expand All @@ -369,7 +369,7 @@ minEdgeLengthToBe1MinFlow = $third_assembly_iter_param.minEdgeLengthToBe1MinFlow
<output name="contigs" value="test2_contigs.fasta" compare="sim_size" delta="5"/>
<output name="scaffolds" value="test2_scaffolds.fasta" compare="sim_size" delta="5"/>
</test>
<test>
<test expect_num_outputs="2">
<conditional name="input_cond">
<param name="library_type" value="single"/>
<param name="inS" value="ecoli_1K_1.fq.gz" ftype="fastq.gz"/>
Expand Down
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