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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
author | iuc |
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date | Mon, 29 Jul 2019 08:47:05 -0400 |
parents | f7a0d41036c7 |
children | cf1ffd88f895 |
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<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.1"> <description>convert SAM to BAM</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ #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> <conditional name="source"> <param label="Choose the source for the reference genome" name="index_source" type="select"> <option value="cached">Use a built-in genome</option> <option value="history">Use a genome from the history</option> </param> <when value="cached"> <param name="input1" type="data" format="sam" label="SAM file to convert"> <validator type="unspecified_build" /> <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" /> </param> <param name="index" type="select" label="Using reference genome"> <options from_data_table="fasta_indexes"> <filter column="1" key="dbkey" ref="input1" type="data_meta" /> <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> </options> </param> </when> <when value="history"> <param name="input1" type="data" format="sam" label="SAM file to convert" /> <param name="ref_file" type="data" format="fasta" label="Using reference file" /> </when> </conditional> </inputs> <outputs> <data name="output1" format="bam" label="${tool.name} on ${on_string}: converted BAM"> <actions> <conditional name="source.index_source"> <when value="cached"> <action name="dbkey" type="metadata"> <option name="source.input1" param_attribute="dbkey" type="from_param" /> </action> </when> <when value="history"> <action name="dbkey" type="metadata"> <option name="source.ref_file" param_attribute="dbkey" type="from_param" /> </action> </when> </conditional> </actions> </data> </outputs> <tests> <test> <param name="index_source" value="history" /> <param name="input1" ftype="sam" value="sam_to_bam_in1.sam" /> <param name="ref_file" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> <output name="output1" ftype="bam" file="sam_to_bam_out1.bam" /> </test> <test> <param name="index_source" value="cached" /> <param name="input1" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" /> <param name="index" value="equCab2chrM" /> <output name="output1" ftype="bam" file="sam_to_bam_out2.bam" /> </test> <test> <param name="index_source" value="history" /> <param name="input1" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> <param name="ref_file" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" /> </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>