Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 16:589620eec35d

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author kkonganti
date Tue, 28 Jun 2022 18:18:17 -0400
parents 676902feecda
children 1cb92deb15f8
comparison
equal deleted inserted replaced
15:676902feecda 16:589620eec35d
4 <requirement type="package" version="22.04">nextflow</requirement> 4 <requirement type="package" version="22.04">nextflow</requirement>
5 <requirement type="package">graphviz</requirement> 5 <requirement type="package">graphviz</requirement>
6 </requirements> 6 </requirements>
7 <version_command>nextflow -version</version_command> 7 <version_command>nextflow -version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 mkdir -p cpipes-input && 9 mkdir -p cpipes-input;
10 #for $key in $input.keys() 10 #for $key in $input.keys()
11 ln -sf '$input[$key]' './cpipes-input/$key'; 11 ln -sf '$input[$key]' './cpipes-input/$key';
12 #end for 12 #end for
13 pwd_path=\$(pwd) && 13 pwd_path=\$(pwd);
14 $__tool_directory__/0.2.1/cpipes 14 $__tool_directory__/0.2.1/cpipes
15 #if ($pipeline == "centriflaken"): 15 #if ($pipeline == "centriflaken"):
16 --pipeline $pipeline 16 --pipeline $pipeline
17 --fq_single_end true 17 --fq_single_end true
18 #elif ($pipeline.name == "centriflaken_hy"): 18 #elif ($pipeline == "centriflaken_hy"):
19 --pipeline $pipeline 19 --pipeline $pipeline
20 #if ($reads_lib_layout == "single"): 20 #if ($reads_lib_layout == "single"):
21 --fq_single_end true 21 --fq_single_end true
22 #else: 22 #else:
23 --fq_single_end false 23 --fq_single_end false
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}"> 63 <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}">
64 <discover_datasets pattern="__designation_and_ext__" assign_primary_output="true" directory="cpipes-output/${pipeline}-multiqc"/> 64 <discover_datasets pattern="(?P&lt;name&gt;.*)\.html" ext="html" assign_primary_output="true" directory="./cpipes-output/${pipeline}-multiqc"/>
65 </data> 65 </data>
66 <data name="assembled_mags" format="fasta" label="CENTRIFLAKEN: Assembled MAGs on ${on_string}"> 66 <data name="assembled_mags" format="fasta" label="CENTRIFLAKEN: Assembled MAGs on ${on_string}">
67 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.assembly_filtered_contigs\.(?P&lt;ext&gt;.+)" visible="true" directory="cpipes-output/${pipeline}-results/kraken2_extract_contigs"/> 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> 68 </data>
69 </outputs> 69 </outputs>
70 <tests> 70 <tests>
71 <!--Test 01: long reads--> 71 <!--Test 01: long reads-->
72 <test expect_num_outputs="2"> 72 <test expect_num_outputs="2">