Mercurial > repos > mvdbeek > bam_readtagger

comparison findcluster.xml @ 40:4b1ebfcd0f46 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
author mvdbeek
date Sun, 01 Apr 2018 03:53:15 -0400
parents f6311a04a6c9
children 4fdf606153df
comparison
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39:432bb619c079 40:4b1ebfcd0f46
1 <tool id="findcluster" name="Find clusters of reads" version="0.4.9"> 1 <tool id="findcluster" name="Find clusters of reads" version="0.4.10">
2 <description>in bam files</description> 2 <description>in bam files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="0.4.9">readtagger</requirement> 7 <requirement type="package" version="0.4.10">readtagger</requirement>
8 </requirements> 8 </requirements>
9 <version_command>findcluster --version</version_command> 9 <version_command>findcluster --version</version_command>
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 #import re 11 #import re
12 #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier)) 12 #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier))
26 --genome_reference_fasta '$genome_source.ref_file' 26 --genome_reference_fasta '$genome_source.ref_file'
27 #else : 27 #else :
28 --genome_bwa_index '$genome_source.ref_file.fields.path' 28 --genome_bwa_index '$genome_source.ref_file.fields.path'
29 #end if 29 #end if
30 #end if 30 #end if
31 --output_bam '$output_bam' 31 #if str($make_bam) == 'True':
32 --output_gff '$output_gff' 32 --output_bam '$output_bam'
33 --output_fasta '$output_fasta' 33 #end if
34 #if str($make_vcf) == 'True'
35 --output_vcf '$output_vcf'
36 #end if
37 #if str($make_gff) == 'True'
38 --output_gff '$output_gff'
39 #end if
40 #if str($make_fasta) == 'True'
41 --output_fasta '$output_fasta'
42 #end if
34 --sample_name '$sample_name' 43 --sample_name '$sample_name'
35 --threads "\${GALAXY_SLOTS:-2}" 44 --threads "\${GALAXY_SLOTS:-2}"
36 ]]></command> 45 ]]></command>
37 <inputs> 46 <inputs>
38 <param name="input" argument="--input_path" type="data" format="bam"/> 47 <param name="input" argument="--input_path" type="data" format="bam"/>
39 48 <param name="make_bam" type="boolean" truevalue="True" checked="true" label="Produce an alignment file containing evidence for insertions."/>
49 <param name="make_vcf" type="boolean" truevalue="True" checked="true" label="Produce a VCF file describing the insertion that have been found."/>
50 <param name="make_gff" type="boolean" truevalue="True" checked="false" label="produce a GFF file describing the insertions that have been found."/>
51 <param name="make_fasta" type="boolean" checked="True" truevalue="True" label="Produce a fasta file containing assembled contigs."/>
40 <expand macro="reference_source_conditional" reference_type="transposon"/> 52 <expand macro="reference_source_conditional" reference_type="transposon"/>
41 <expand macro="reference_source_conditional" reference_type="genome"/> 53 <expand macro="reference_source_conditional" reference_type="genome"/>
42 </inputs> 54 </inputs>
43 <outputs> 55 <outputs>
44 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/> 56 <data name="output_bam" format="bam" label="findcluster BAM on $on_string">
45 <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string"/> 57 <filter>make_bam</filter>
46 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/> 58 </data>
59 <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string">
60 <filter>make_fasta</filter>
61 </data>
62 <data name="output_vcf" format="vcf" label="findcluster VCF on $on_string">
63 <filter>make_vcf</filter>
64 </data>
65 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string">
66 <filter>make_gff</filter>
67 </data>
47 </outputs> 68 </outputs>
48 <tests> 69 <tests>
49 <test> 70 <test>
50 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> 71 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
72 <param name="make_gff" value="true"/>
51 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/> 73 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
52 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0" sort="True"/> 74 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" compare="sim_size"/>
75 <output name="output_vcf" file="three_cluster_out.vcf" ftype="vcf" compare="sim_size"/>
53 </test> 76 </test>
54 <test> 77 <test>
55 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> 78 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
56 <param name="transposon_source|reference_source_selector" value="history"/> 79 <param name="transposon_source|reference_source_selector" value="history"/>
57 <param name="transposon_source|ref_file" value="reference.fasta" ftype="fasta"/> 80 <param name="transposon_source|ref_file" value="reference.fasta" ftype="fasta"/>
81 <param name="make_gff" value="true"/>
58 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/> 82 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
59 <output name="output_gff"> 83 <output name="output_gff">
60 <assert_contents> 84 <assert_contents>
61 <has_text text="FBti0019066_rover_Gypsy" /> 85 <has_text text="FBti0019066_rover_Gypsy" />
62 </assert_contents> 86 </assert_contents>