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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author | iuc |
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date | Sun, 08 Sep 2024 03:25:11 +0000 |
parents | 9bd1568619cd |
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<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.2" profile="@PROFILE@"> <description>convert SAM to BAM</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @ADDTHREADS@ @ADDMEMORY@ @PREPARE_FASTA_IDX@ samtools view -b -@ \$addthreads -t "\$reffai" '$input' | samtools sort -O bam -@ \$addthreads -m \$addmemory"M" -o '$output1' -T "\${TMPDIR:-.}" ]]></command> <inputs> <param name="input" type="data" format="sam" label="SAM file to convert"/> <expand macro="mandatory_reference" argument="-t"/> </inputs> <outputs> <data name="output1" format="bam" label="${tool.name} on ${on_string}: converted BAM"> <actions> <conditional name="addref_cond.addref_select"> <when value="cached"> <action name="dbkey" type="metadata"> <option name="input" param_attribute="dbkey" type="from_param" /> </action> </when> <when value="history"> <action name="dbkey" type="metadata"> <option name="addref_cond.ref" param_attribute="dbkey" type="from_param" /> </action> </when> </conditional> </actions> </data> </outputs> <tests> <test> <param name="addref_select" value="history" /> <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> <param name="input" ftype="sam" value="sam_to_bam_in1.sam" /> <output name="output1" ftype="bam" file="sam_to_bam_out1.bam" lines_diff="4"/> </test> <test> <param name="addref_select" value="cached" /> <param name="ref" value="equCab2chrM" /> <param name="input" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" /> <output name="output1" ftype="bam" file="sam_to_bam_out2.bam" lines_diff="4"/> </test> <test> <param name="addref_select" value="history" /> <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> </test> <test> <!-- Test direct use of bgzipped reference --> <param name="addref_select" value="history" /> <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.bgzipped_fasta.gz" /> <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> </test> <test> <!-- Test with simple gzipped reference, which requires decompression --> <param name="addref_select" value="history" /> <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.fasta.gz" /> <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> </test> </tests> <help><![CDATA[ **What it does** Converts SAM dataset into its binary, BAM, representation using the ``samtools view`` and ``sort`` commands. ]]></help> <expand macro="citations"/> </tool>