Mercurial > repos > devteam > sam_to_bam
diff sam_to_bam.xml @ 7:881e16ad05c6 draft
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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--- a/sam_to_bam.xml Tue Apr 21 14:52:20 2015 -0400 +++ b/sam_to_bam.xml Wed Nov 11 12:51:52 2015 -0500 @@ -1,22 +1,21 @@ -<tool id="sam_to_bam" name="SAM-to-BAM" version="2.0"> +<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1"> <description>convert SAM to BAM</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"></expand> + <expand macro="stdio"></expand> <expand macro="version_command"></expand> - <expand macro="stdio"></expand> <command> <![CDATA[ - samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o sorted_input.bam -T temp "$input1" && - #if $source.index_source == "history": - ln -s $source.ref_file input.fa && - samtools faidx input.fa && - #else - ln -s ${source.index.fields.path} input.fa && - ln -s ${source.index.fields.path}.fai input.fa.fai && - #end if - samtools view -@ \${GALAXY_SLOTS:-1} -b -h -o $output1 -T input.fa sorted_input.bam + #if $source.index_source == "history": + ln -s $source.ref_file input.fa && + samtools faidx input.fa && + #else + ln -s ${source.index.fields.path} input.fa && + ln -s ${source.index.fields.path}.fai input.fa.fai && + #end if + samtools view -b -@ \${GALAXY_SLOTS:-1} -t input.fa.fai "$input1" | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o "$output1" -T temp ]]> </command> <inputs> @@ -68,6 +67,12 @@ <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" /> <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" /> </test> + <test> + <param name="index_source" value="history" /> + <param name="input1" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> + <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" /> + <output file="sam_to_bam_out3.bam" ftype="bam" name="output1" /> + </test> </tests> <help> <![CDATA[