Mercurial > repos > devteam > sam_to_bam
diff sam_to_bam.xml @ 4:4afb4a5f0924 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author | iuc |
---|---|
date | Tue, 09 May 2017 11:18:00 -0400 |
parents | 5a5f92086188 |
children | a832dc88e7dc |
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--- a/sam_to_bam.xml Fri Dec 18 19:42:41 2015 -0500 +++ b/sam_to_bam.xml Tue May 09 11:18:00 2017 -0400 @@ -1,23 +1,34 @@ -<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> - <command> - <![CDATA[ +<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 $source.ref_file input.fa && - samtools faidx input.fa && + ln -s '${source.ref_file}' input.fa && + samtools faidx input.fa && #else - ln -s ${source.index.fields.path} input.fa && - ln -s ${source.index.fields.path}.fai input.fa.fai && + ln -s '${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 "$output1" -T temp - ]]> - </command> + + samtools view + -b + -@ \${GALAXY_SLOTS:-1} + -t input.fa.fai '$input1' | + + samtools sort + -O bam + -@ \${GALAXY_SLOTS:-1} + -o '$output1' + -T temp + ]]></command> + <inputs> <conditional name="source"> <param label="Choose the source for the reference genome" name="index_source" type="select"> @@ -25,11 +36,11 @@ <option value="history">Use a genome from the history</option> </param> <when value="cached"> - <param format="sam" label="SAM file to convert" metadata_name="dbkey" name="input1" type="data"> + <param name="input1" type="data" format="sam" label="SAM file to convert"> <validator type="unspecified_build" /> <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" /> </param> - <param label="Using reference genome" name="index" type="select"> + <param name="index" type="select" label="Using reference genome"> <options from_data_table="fasta_indexes"> <filter column="1" key="dbkey" ref="input1" type="data_meta" /> <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> @@ -37,13 +48,13 @@ </param> </when> <when value="history"> - <param format="sam" label="SAM file to convert" name="input1" type="data" /> - <param format="fasta" label="Using reference file" metadata_name="dbkey" name="ref_file" type="data" /> + <param name="input1" type="data" format="sam" label="SAM file to convert" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> </when> </conditional> </inputs> <outputs> - <data format="bam" label="${tool.name} on ${on_string}: converted BAM" name="output1"> + <data name="output1" format="bam" label="${tool.name} on ${on_string}: converted BAM"> <actions> <conditional name="source.index_source"> <when value="cached"> @@ -64,26 +75,26 @@ <test> <param name="index_source" value="history" /> <param name="input1" ftype="sam" value="sam_to_bam_in1.sam" /> - <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" /> - <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" /> + <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 dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" /> - <output file="sam_to_bam_out3.bam" ftype="bam" name="output1" /> + <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[ + <help><![CDATA[ **What it does** -Converts SAM dataset into its binary, BAM, representation using ``samtools sort`` and ``view`` commands:: - - samtools sort -O bam -o sorted_input.bam [INPUT SAM] - samtools view -b -h -o -T [REFERENCE GENOME] [OUTPUT BAM] sorted_input.bam - -]]> - </help> - <expand macro="citations"></expand> +Converts SAM dataset into its binary, BAM, representation using the ``samtools view`` and ``sort`` commands. + ]]></help> + <expand macro="citations"/> </tool>