Mercurial > repos > iuc > colibread_commet
comparison commet.xml @ 6:4daa32d21ea5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
| author | iuc |
|---|---|
| date | Sat, 05 Oct 2024 19:55:07 +0000 |
| parents | d03353742508 |
| children |
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| 5:d03353742508 | 6:4daa32d21ea5 |
|---|---|
| 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** |