Mercurial > repos > devteam > sam_to_bam
changeset 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 |
| files | macros.xml sam_to_bam.xml test-data/sam_to_bam_out1.bam test-data/sam_to_bam_out2.bam test-data/sam_to_bam_out3.bam |
| diffstat | 5 files changed, 96 insertions(+), 68 deletions(-) [+] |
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--- a/macros.xml Thu Oct 10 03:39:03 2019 -0400 +++ b/macros.xml Tue Sep 28 15:58:15 2021 +0000 @@ -5,10 +5,16 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">1.9</token> - <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> + <token name="@TOOL_VERSION@">1.13</token> + <token name="@PROFILE@">20.05</token> + <token name="@FLAGS@"><![CDATA[ + #set $flags = 0 + #if $filter + #set $flags = sum(map(int, str($filter).split(','))) + #end if + ]]></token> <token name="@PREPARE_IDX@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices ln -s '$input' infile && #if $input.is_of_type('bam'): #if str( $input.metadata.bam_index ) != "None": @@ -25,7 +31,7 @@ #end if ]]></token> <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices #for $i, $bam in enumerate( $input_bams ): ln -s '$bam' '${i}' && #if $bam.is_of_type('bam'): @@ -63,6 +69,51 @@ #set reffai=None #end if ]]></token> + + <xml name="optional_reference"> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="no">No</option> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="no"/> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + </options> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/> + </param> + </when> + </conditional> + </xml> + <xml name="mandatory_reference" token_help="" token_argument=""> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> + </options> + </param> + </when> + </conditional> + </xml> + + <token name="@ADDTHREADS@"><![CDATA[ ##compute the number of ADDITIONAL threads to be used by samtools (-@) addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && @@ -70,28 +121,28 @@ <token name="@ADDMEMORY@"><![CDATA[ ##compute the number of memory available to samtools sort (-m) ##use only 75% of available: https://github.com/samtools/samtools/issues/831 - addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && + addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ]]></token> <xml name="seed_input"> - <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> + <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> </xml> - <xml name="flag_options"> - <option value="1">read is paired</option> - <option value="2">read is mapped in a proper pair</option> - <option value="4">read is unmapped</option> - <option value="8">mate is unmapped</option> - <option value="16">read reverse strand</option> - <option value="32">mate reverse strand</option> - <option value="64">read is the first in a pair</option> - <option value="128">read is the second in a pair</option> - <option value="256">alignment or read is not primary</option> - <option value="512">read fails platform/vendor quality checks</option> - <option value="1024">read is a PCR or optical duplicate</option> - <option value="2048">supplementary alignment</option> + <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false"> + <option value="1" selected="@S1@">Read is paired</option> + <option value="2" selected="@S2@">Read is mapped in a proper pair</option> + <option value="4" selected="@S4@">Read is unmapped</option> + <option value="8" selected="@S8@">Mate is unmapped</option> + <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option> + <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option> + <option value="64" selected="@S64@">Read is the first in a pair</option> + <option value="128" selected="@S128@">Read is the second in a pair</option> + <option value="256" selected="@S256@">Alignment of the read is not primary</option> + <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option> + <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option> + <option value="2048" selected="@S2048@">Alignment is supplementary</option> </xml> - <!-- region specification macros and tokens for tools that allow the specification + <!-- region specification macros and tokens for tools that allow the specification of region by bed file / space separated list of regions --> <token name="@REGIONS_FILE@"><![CDATA[ #if $cond_region.select_region == 'tab':
--- 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[