Mercurial > repos > iuc > colibread_commet

comparison commet.xml @ 6:5918765a6426 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
author iuc
date Sat, 05 Oct 2024 19:53:07 +0000
parents 701b1ab185fe
children
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5:701b1ab185fe 6:5918765a6426
1 <tool id="commet" name="Commet" version="24.7.14+galaxy0" profile="@PROFILE@"> 1 <tool id="commet" name="Commet" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>COmpare Multiple METagenomes</description> 2 <description>COmpare Multiple METagenomes</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">24.7.14</token>
4 <import>macros.xml</import> 5 <import>macros.xml</import>
5 </macros> 6 </macros>
6 <requirements> 7 <requirements>
7 <requirement type="package" version="24.7.14">commet</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">commet</requirement>
8 </requirements> 9 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 #for $i, $set in enumerate($sets): 11 #for $i, $set in enumerate($sets):
11 echo "set${i}: ${ ','.join(['%s' % read for read in $set.reads]) }" >> commet_input_sets.txt && 12 echo "set${i}: ${ ','.join(['%s' % read for read in $set.reads]) }" >> commet_input_sets.txt &&
12 #end for 13 #end for
43 <param name="normalized_outputs" label="Generate normalized files" type="boolean" checked="true"/> 44 <param name="normalized_outputs" label="Generate normalized files" type="boolean" checked="true"/>
44 <param name="plain_outputs" label="Generate plain files" type="boolean" checked="false"/> 45 <param name="plain_outputs" label="Generate plain files" type="boolean" checked="false"/>
45 <param name="percentage_outputs" label="Generate percentage files" type="boolean" checked="false"/> 46 <param name="percentage_outputs" label="Generate percentage files" type="boolean" checked="false"/>
46 </inputs> 47 </inputs>
47 <outputs> 48 <outputs>
48 <data format="csv" name="matrix_plain" from_work_dir="output_commet/matrix_plain.csv" label="Matrix plain with ${tool.name} on ${on_string}" > 49 <data format="csv" name="matrix_plain" from_work_dir="output_commet/matrix_plain.csv" label="${tool.name} on ${on_string}: Matrix plain" >
49 <filter>plain_outputs</filter> 50 <filter>plain_outputs</filter>
50 </data> 51 </data>
51 <data format="csv" name="matrix_percentage" from_work_dir="output_commet/matrix_percentage.csv" label="Matrix percentage with ${tool.name} on ${on_string}" > 52 <data format="csv" name="matrix_percentage" from_work_dir="output_commet/matrix_percentage.csv" label="${tool.name} on ${on_string}: Matrix percentage" >
52 <filter>percentage_outputs</filter> 53 <filter>percentage_outputs</filter>
53 </data> 54 </data>
54 <data format="csv" name="matrix_normalized" from_work_dir="output_commet/matrix_normalized.csv" label="Matrix normalized with ${tool.name} on ${on_string}" > 55 <data format="csv" name="matrix_normalized" from_work_dir="output_commet/matrix_normalized.csv" label="${tool.name} on ${on_string}: Matrix normalized" >
55 <filter>normalized_outputs</filter> 56 <filter>normalized_outputs</filter>
56 </data> 57 </data>
57 <data format="png" name="dendrogram_normalized" from_work_dir="output_commet/dendrogram_normalized.png" label="Dendrogram ${tool.name} on ${on_string}" /> 58 <data format="png" name="dendrogram_normalized" from_work_dir="output_commet/dendrogram_normalized.png" label="${tool.name} on ${on_string}: Dendrogram" />
58 <data format="png" name="heatmap_normalized" from_work_dir="output_commet/heatmap_normalized.png" label="Heatmap normalized with ${tool.name} on ${on_string}" > 59 <data format="png" name="heatmap_normalized" from_work_dir="output_commet/heatmap_normalized.png" label="${tool.name} on ${on_string}: Heatmap normalized" >
59 <filter>normalized_outputs</filter> 60 <filter>normalized_outputs</filter>
60 </data> 61 </data>
61 <data format="png" name="heatmap_percentage" from_work_dir="output_commet/heatmap_percentage.png" label="Heatmap percentage with ${tool.name} on ${on_string}" > 62 <data format="png" name="heatmap_percentage" from_work_dir="output_commet/heatmap_percentage.png" label="${tool.name} on ${on_string}: Heatmap percentage" >
62 <filter>percentage_outputs</filter> 63 <filter>percentage_outputs</filter>
63 </data> 64 </data>
64 <data format="png" name="heatmap_plain" from_work_dir="output_commet/heatmap_plain.png" label="Heatmap Plain with ${tool.name} on ${on_string}" > 65 <data format="png" name="heatmap_plain" from_work_dir="output_commet/heatmap_plain.png" label="${tool.name} on ${on_string}: Heatmap Plain" >
65 <filter>plain_outputs</filter> 66 <filter>plain_outputs</filter>
66 </data> 67 </data>
67 </outputs> 68 </outputs>
68 <tests> 69 <tests>
69 <test> 70 <test expect_num_outputs="5">
70 <param name="input_type" value="list" />
71 <repeat name="sets"> 71 <repeat name="sets">
72 <param name="reads" value="commet/A.fa.gz" ftype="fasta.gz" /> 72 <param name="reads" value="commet/A.fa.gz" ftype="fasta.gz" />
73 </repeat> 73 </repeat>
74 <repeat name="sets"> 74 <repeat name="sets">
75 <param name="reads" value="commet/B.fa.gz,commet/C.fa.gz" ftype="fasta.gz" /> 75 <param name="reads" value="commet/B.fa.gz,commet/C.fa.gz" ftype="fasta.gz" />
78 <param name="reads" value="commet/D.fa.gz" ftype="fasta.gz" /> 78 <param name="reads" value="commet/D.fa.gz" ftype="fasta.gz" />
79 </repeat> 79 </repeat>
80 <param name="plain_outputs" value="True"/> 80 <param name="plain_outputs" value="True"/>
81 <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/> 81 <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/>
82 <output name="matrix_plain" file="commet/matrix_plain.csv"/> 82 <output name="matrix_plain" file="commet/matrix_plain.csv"/>
83 <output name="heatmap_plain">
84 <assert_contents>
85 <has_size size="1k"/>
86 </assert_contents>
87 </output>
83 </test> 88 </test>
84 </tests> 89 </tests>
85 <help><![CDATA[ 90 <help><![CDATA[
86 91
87 **Description** 92 **Description**