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comparison sam_to_bam.xml @ 7:881e16ad05c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/sam_to_bam commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:51:52 -0500
parents d04d9f1c6791
children f7a0d41036c7
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6:d04d9f1c6791 7:881e16ad05c6
1 <tool id="sam_to_bam" name="SAM-to-BAM" version="2.0"> 1 <tool id="sam_to_bam" name="SAM-to-BAM" version="2.1">
2 <description>convert SAM to BAM</description> 2 <description>convert SAM to BAM</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
7 <expand macro="version_command"></expand> 8 <expand macro="version_command"></expand>
8 <expand macro="stdio"></expand>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o sorted_input.bam -T temp "$input1" && 11 #if $source.index_source == "history":
12 #if $source.index_source == "history": 12 ln -s $source.ref_file input.fa &&
13 ln -s $source.ref_file input.fa && 13 samtools faidx input.fa &&
14 samtools faidx input.fa && 14 #else
15 #else 15 ln -s ${source.index.fields.path} input.fa &&
16 ln -s ${source.index.fields.path} input.fa && 16 ln -s ${source.index.fields.path}.fai input.fa.fai &&
17 ln -s ${source.index.fields.path}.fai input.fa.fai && 17 #end if
18 #end if 18 samtools view -b -@ \${GALAXY_SLOTS:-1} -t input.fa.fai "$input1" | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o "$output1" -T temp
19 samtools view -@ \${GALAXY_SLOTS:-1} -b -h -o $output1 -T input.fa sorted_input.bam
20 ]]> 19 ]]>
21 </command> 20 </command>
22 <inputs> 21 <inputs>
23 <conditional name="source"> 22 <conditional name="source">
24 <param label="Choose the source for the reference genome" name="index_source" type="select"> 23 <param label="Choose the source for the reference genome" name="index_source" type="select">
66 <param name="index_source" value="history" /> 65 <param name="index_source" value="history" />
67 <param name="input1" ftype="sam" value="sam_to_bam_in1.sam" /> 66 <param name="input1" ftype="sam" value="sam_to_bam_in1.sam" />
68 <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" /> 67 <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
69 <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" /> 68 <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" />
70 </test> 69 </test>
70 <test>
71 <param name="index_source" value="history" />
72 <param name="input1" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
73 <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
74 <output file="sam_to_bam_out3.bam" ftype="bam" name="output1" />
75 </test>
71 </tests> 76 </tests>
72 <help> 77 <help>
73 <![CDATA[ 78 <![CDATA[
74 **What it does** 79 **What it does**
75 80