Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 18:4f31b641f6fd

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"planemo upload"
author kkonganti
date Tue, 28 Jun 2022 20:38:30 -0400
parents 1cb92deb15f8
children 2671e2d54a25
comparison
equal deleted inserted replaced
17:1cb92deb15f8 18:4f31b641f6fd
59 <option value="cingularitygac">singularity</option> 59 <option value="cingularitygac">singularity</option>
60 </param> 60 </param>
61 </inputs> 61 </inputs>
62 <outputs> 62 <outputs>
63 <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}" from_work_dir="./cpipes-output/${pipeline}-multiqc/multiqc_report.html"/> 63 <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}" from_work_dir="./cpipes-output/${pipeline}-multiqc/multiqc_report.html"/>
64 <!-- <discover_datasets pattern="(?P&lt;name&gt;.*)\.html" ext="html" assign_primary_output="true" directory="./cpipes-output/${pipeline}-multiqc"/> --> 64 <collection name="assembled_mags" type="list" label="CENTRIFLAKEN: Assembled MAGs on ${on_string}">
65 <!-- </data> --> 65 <discover_datasets pattern="(?P&lt;name&gt;.*)\.assembly_filtered_contigs\.fasta" ext="fasta" directory="./cpipes-output/${pipeline}-results/kraken2_extract_contigs"/>
66 <data name="assembled_mags" format="fasta" label="CENTRIFLAKEN: Assembled MAGs on ${on_string}"> 66 </collection>
67 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.assembly_filtered_contigs\.fasta" ext="fasta" visible="true" directory="./cpipes-output/${pipeline}-results/kraken2_extract_contigs"/>
68 </data>
69 </outputs> 67 </outputs>
70 <tests> 68 <tests>
71 <!--Test 01: long reads--> 69 <!--Test 01: long reads-->
72 <test expect_num_outputs="2"> 70 <test expect_num_outputs="2">
73 <param name="input"> 71 <param name="input">
77 <element name="FAL11342.fastq.gz" value="FAL11342.fastq.gz" /> 75 <element name="FAL11342.fastq.gz" value="FAL11342.fastq.gz" />
78 </collection> 76 </collection>
79 </param> 77 </param>
80 <param name="fq_suffix" value=".fastq.gz"/> 78 <param name="fq_suffix" value=".fastq.gz"/>
81 <output name="multiqc_report" file="multiqc_report.html" ftype="html" compare="sim_size"/> 79 <output name="multiqc_report" file="multiqc_report.html" ftype="html" compare="sim_size"/>
82 <output name="assembled_mags" file="FAL11127.assembly_filtered.contigs.fasta" ftype="fasta" compare="sim_size"/> 80 <!-- <output name="assembled_mags" file="FAL11127.assembly_filtered.contigs.fasta" ftype="fasta" compare="sim_size"/> -->
83 </test> 81 </test>
84 </tests> 82 </tests>
85 <help><![CDATA[ 83 <help><![CDATA[
86 84
87 .. class:: infomark 85 .. class:: infomark