Mercurial > repos > devteam > samtools_calmd
changeset 5:c147e3a10573 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
| author | iuc |
|---|---|
| date | Tue, 28 Sep 2021 16:12:02 +0000 |
| parents | 06dc50b7b711 |
| children | 92ec40abcdcf |
| files | macros.xml samtools_calmd.xml test-data/samtools_calmd_out_1.bam test-data/samtools_calmd_out_2.bam |
| diffstat | 4 files changed, 86 insertions(+), 57 deletions(-) [+] |
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--- a/macros.xml Thu Oct 17 02:18:43 2019 -0400 +++ b/macros.xml Tue Sep 28 16:12:02 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/samtools_calmd.xml Thu Oct 17 02:18:43 2019 -0400 +++ b/samtools_calmd.xml Tue Sep 28 16:12:02 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_calmd" name="CalMD" version="2.0.2"> +<tool id="samtools_calmd" name="Samtools calmd" version="2.0.3" profile="@PROFILE@"> <description>recalculate MD/NM tags</description> <macros> <import>macros.xml</import> @@ -8,13 +8,7 @@ <expand macro="version_command"/> <command><![CDATA[ @ADDTHREADS@ -#if str( $reference_source.reference_source_selector ) == "history": - #set ref_fa = 'ref.fa' - ln -s '${reference_source.ref_fasta}' ref.fa && - samtools faidx ref.fa && -#else: - #set ref_fa = str( $reference_source.ref_fasta.fields.path ) -#end if +@PREPARE_FASTA_IDX@ samtools calmd $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq @@ -23,29 +17,13 @@ #end if -b -@ \$addthreads - '$input_bam' - '$ref_fa' + '$input' + '$reffa' > '$calmd_output' ]]></command> <inputs> - <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" /> - <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> - <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="ref_fasta" type="select" label="Using reference genome"> - <options from_data_table="fasta_indexes"> - <filter type="data_meta" column="dbkey" key="dbkey" ref="input_bam" /> - <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> - </options> - </param> - </when> - <when value="history"> - <param name="ref_fasta" type="data" format="fasta" label="Using reference file" /> - </when> - </conditional> + <param name="input" type="data" format="bam" label="BAM file to recalculate" /> + <expand macro="mandatory_reference"/> <conditional name="baq_settings"> <param name="use_baq" argument="-r" type="select" label="Do you also want BAQ (Base Alignment Quality) scores to be calculated?"> @@ -86,10 +64,10 @@ <test> <param name="use_baq" value="" /> <param name="option_sets" value="default" /> - <param name="input_bam" value="phiX.bam"/> - <param name="reference_source_selector" value="history" /> - <param name="ref_fasta" value="phiX.fasta" /> - <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> + <param name="input" value="phiX.bam"/> + <param name="addref_select" value="history" /> + <param name="ref" value="phiX.fasta" /> + <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" lines_diff="4" /> </test> <test> <param name="use_baq" value="-r" /> @@ -97,10 +75,10 @@ <param name="option_sets" value="advanced" /> <param name="change_identical" value="true" /> <param name="adjust_mq" value="50" /> - <param name="input_bam" value="phiX.bam"/> - <param name="reference_source_selector" value="history" /> - <param name="ref_fasta" value="phiX.fasta" /> - <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> + <param name="input" value="phiX.bam"/> + <param name="addref_select" value="history" /> + <param name="ref" value="phiX.fasta" /> + <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" lines_diff="4" /> </test> </tests> <help><![CDATA[ @@ -125,7 +103,7 @@ MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7 NM (integer) Edit distance to the reference, including ambiguous bases but excluding clipping - BQ (string) String of offsets to base alignment quality (BAQ), of the same length as the read sequence. + BQ (string) String of offsets to base alignment quality (BAQ), of the same length as the read sequence. At the i-th read base, BAQ i = Q i − (BQ i − 64) where Q i is the i-th base quality. See references for more information about SAM format tags.