Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 3:3154e7efa1c4

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"planemo upload"
author kkonganti
date Mon, 27 Jun 2022 18:19:22 -0400
parents 29a590703d3e
children 34d3ef477de3
comparison
equal deleted inserted replaced
2:29a590703d3e 3:3154e7efa1c4
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 $input in $LIST 10 #for $input_dataset in $input
11 ln -sf '$input' './cpipes-input/${input.element_identifier}'; 11 ln -sf '$input_dataset' './cpipes-input/${input.element_identifier}';
12 #end for 12 #end for
13 pwd_path=\$(pwd) && 13 pwd_path=\$(pwd) &&
14 $__tool_directory__/0.2.1/cpipes 14 $__tool_directory__/0.2.1/cpipes
15 #if (reads.type == "long"): 15 #if (reads.type == "long"):
16 --pipeline centriflaken 16 --pipeline centriflaken
17 #else: 17 #else:
18 --pipeline centriflaken_hy 18 --pipeline centriflaken_hy
19 #end if 19 #end if
20 --input \${pwd_path}/cpipes-input 20 --input \${pwd_path}/cpipes-input
21 --output \${pwd_path}/cpipes-output 21 --output \${pwd_path}/cpipes-output
22 #if ($reads_lib.paired_end == "true"): 22 #if ($reads.reads_lib.paired_end == "true"):
23 --fq_single_end false 23 --fq_single_end false
24 --fq_suffix '${fq_suffix}' 24 --fq_suffix '${reads.reads_lib.fq_suffix}'
25 --fq2_suffix '${fq2_suffix}' 25 --fq2_suffix '${reads.reads_lib.fq2_suffix}'
26 #else: 26 #else:
27 --fq_single_end true 27 --fq_single_end true
28 --fq_suffix '${fq_suffix}' 28 --fq_suffix '${reads.fq_suffix}'
29 #end if 29 #end if
30 --fq_filename_delim '${fq_filename_delim}' 30 --fq_filename_delim '${fq_filename_delim}'
31 --fq_filename_delim_idx $fq_filename_delim_idx 31 --fq_filename_delim_idx $fq_filename_delim_idx
32 --centrifuge_extract_bug '${centrifuge_extract_bug}' 32 --centrifuge_extract_bug '${centrifuge_extract_bug}'
33 --flye_genome_size '${genome_size}' 33 --flye_genome_size '${genome_size}'
34 -profile $profile 34 -profile $profile
35 ]]></command> 35 ]]></command>
36 <inputs> 36 <inputs>
37 <param name="input" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input reads" /> 37 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" />
38 <conditional name="reads"> 38 <conditional name="reads">
39 <param name="type" type="select" label="Sequencing Read Library Type" value="long"> 39 <param name="type" type="select" label="Sequencing Read Library Type" value="long">
40 <option value="long">Long reads</option> 40 <option value="long">Long reads</option>
41 <option value="short">Short reads</option> 41 <option value="short">Short reads</option>
42 </param> 42 </param>
77 </data> 77 </data>
78 <data name="assembled_mags" format="fasta" label="CENTRIFLAKEN: Assembled MAGs"> 78 <data name="assembled_mags" format="fasta" label="CENTRIFLAKEN: Assembled MAGs">
79 <discover_datasets pattern=".*\.assembly_filtered_contigs.fasta" visible="true" directory="cpipes-output"/> 79 <discover_datasets pattern=".*\.assembly_filtered_contigs.fasta" visible="true" directory="cpipes-output"/>
80 </data> 80 </data>
81 </outputs> 81 </outputs>
82 <tests>
83 <!--Test 01: long reads-->
84 <test expect_num_outputs="2">
85 <param name="input" value="FAL11127.fastq.gz" >
86 <collection type="list">
87 <element name="file1" value="FAL11127.fastq.gz" />
88 <element name="file2" value="FAL11341.fastq.gz" />
89 <element name="file3" value="FAL11342.fastq.gz" />
90 </collection>
91 </param>
92 <param name="fq_suffix" value=".fastq.gz"/>
93 <output name="multiqc_report" file="multiqc_report.html" ftype="html" compare="sim_size"/>
94 <output name="assembled_mags" file="FAL11127.assembly_filtered.contigs.fasta" ftype="fasta" compare="sim_size"/>
95 </test>
96 </tests>
82 <help><![CDATA[ 97 <help><![CDATA[
83 98
84 .. class:: infomark 99 .. class:: infomark
85 100
86 **Purpose** 101 **Purpose**