Mercurial > repos > devteam > sam_to_bam
diff sam_to_bam.xml @ 8:c701f5f96f32 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author | iuc |
---|---|
date | Tue, 28 Sep 2021 15:58:15 +0000 |
parents | 428d5c102c96 |
children | d83ad701f011 |
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--- a/sam_to_bam.xml Thu Oct 10 03:39:03 2019 -0400 +++ b/sam_to_bam.xml Tue Sep 28 15:58:15 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.1"> +<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.2" profile="@PROFILE@"> <description>convert SAM to BAM</description> <macros> @@ -9,62 +9,39 @@ <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 + @ADDTHREADS@ + @ADDMEMORY@ + @PREPARE_FASTA_IDX@ samtools view -b - -@ \${GALAXY_SLOTS:-1} - -t input.fa.fai '$input1' | + -@ \$addthreads + -t '$reffai' + '$input' | samtools sort -O bam - -@ \${GALAXY_SLOTS:-1} + -@ \$addthreads -m \$addmemory"M" -o '$output1' -T "\${TMPDIR:-.}" ]]></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="dbkey" 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> + <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="source.index_source"> + <conditional name="addref_cond.addref_select"> <when value="cached"> <action name="dbkey" type="metadata"> - <option name="source.input1" param_attribute="dbkey" type="from_param" /> + <option name="input" 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" /> + <option name="addref_cond.ref" param_attribute="dbkey" type="from_param" /> </action> </when> </conditional> @@ -73,22 +50,22 @@ </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" /> + <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="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" /> + <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="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" /> + <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> </tests> <help><![CDATA[