Mercurial > repos > iuc > samtools_fixmate
changeset 1:595ae1ba934a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
| author | iuc |
|---|---|
| date | Tue, 28 Sep 2021 16:13:23 +0000 |
| parents | bc0cc7bfbfe9 |
| children | 41e36c99a008 |
| files | macros.xml samtools_fixmate.xml test-data/2_isize_overflow.bam.expected test-data/3_reverse_read_pp_lt.bam.expected test-data/4_reverse_read_pp_equal.bam.expected test-data/5_ct.bam.expected test-data/6_ct_replace.bam.expected test-data/7_two_read_mapped.bam.expected |
| diffstat | 8 files changed, 111 insertions(+), 60 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Fri Sep 28 04:28:45 2018 -0400 +++ b/macros.xml Tue Sep 28 16:13:23 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_fixmate.xml Fri Sep 28 04:28:45 2018 -0400 +++ b/samtools_fixmate.xml Tue Sep 28 16:13:23 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@"> +<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>fill mate coordinates, ISIZE and mate related flags</description> <macros> <import>macros.xml</import> @@ -8,11 +8,11 @@ <expand macro="version_command"/> <command><![CDATA[ @ADDTHREADS@ - ## name sort input + ## name sort input #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'): samtools sort - -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp - -n + -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" + -n -O BAM -o namesorted.bam '$bamfile' && @@ -38,44 +38,44 @@ <param name="addms" type="boolean" argument="-m" truevalue="-m" falsevalue="" checked="false" label="Add ms (mate score) tags" help="These are used by markdup to select the best reads to keep." /> </inputs> <outputs> - <!--<data name="output" format="sam" />--> - <data name="output" format="qname_sorted.bam"/> + <!--<data name="output" format="sam" />--> + <data name="output" format="qname_sorted.bam"/> </outputs> <tests> -<!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493--> -<!-- test_cmd($opts,out=>'fixmate/1_coord_sort.sam.expected', err=>'fixmate/1_coord_sort.sam.expected.err', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/1_coord_sort.sam -", expect_fail=>1);--> -<test> - <param name="bamfile" value="2_isize_overflow.sam" /> - <output name="output" file="2_isize_overflow.bam.expected" /> -</test> -<!-- test_cmd($opts,out=>'fixmate/2_isize_overflow.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/2_isize_overflow.sam -");--> -<test> - <param name="bamfile" value="3_reverse_read_pp_lt.sam" /> - <output name="output" file="3_reverse_read_pp_lt.bam.expected" /> -</test> -<!-- test_cmd($opts,out=>'fixmate/3_reverse_read_pp_lt.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/3_reverse_read_pp_lt.sam -");--> -<test> - <param name="bamfile" value="4_reverse_read_pp_equal.sam" /> - <output name="output" file="4_reverse_read_pp_equal.bam.expected" /> -</test> -<!-- test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");--> -<test> - <param name="bamfile" value="5_ct.sam" /> - <param name="tempcigar" value="-c" /> - <output name="output" file="5_ct.bam.expected" /> -</test> -<!-- test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");--> -<test> - <param name="bamfile" value="6_ct_replace.sam" /> - <param name="tempcigar" value="-c" /> - <output name="output" file="6_ct_replace.bam.expected" /> -</test> -<!-- test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");--> -<test> - <param name="bamfile" value="7_two_read_mapped.sam" /> - <output name="output" file="7_two_read_mapped.bam.expected" /> -</test> -<!--test_cmd($opts,out=>'fixmate/7_two_read_mapped.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/7_two_read_mapped.sam -");--> + <!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493--> + <!-- test_cmd($opts,out=>'fixmate/1_coord_sort.sam.expected', err=>'fixmate/1_coord_sort.sam.expected.err', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/1_coord_sort.sam -", expect_fail=>1);--> + <test> + <param name="bamfile" value="2_isize_overflow.sam" ftype="sam" /> + <output name="output" file="2_isize_overflow.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> + </test> + <!-- test_cmd($opts,out=>'fixmate/2_isize_overflow.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/2_isize_overflow.sam -");--> + <test> + <param name="bamfile" value="3_reverse_read_pp_lt.sam" ftype="sam" /> + <output name="output" file="3_reverse_read_pp_lt.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> + </test> + <!-- test_cmd($opts,out=>'fixmate/3_reverse_read_pp_lt.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/3_reverse_read_pp_lt.sam -");--> + <test> + <param name="bamfile" value="4_reverse_read_pp_equal.sam" ftype="sam" /> + <output name="output" file="4_reverse_read_pp_equal.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> + </test> + <!-- test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");--> + <test> + <param name="bamfile" value="5_ct.sam" ftype="sam" /> + <param name="tempcigar" value="-c" /> + <output name="output" file="5_ct.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> + </test> + <!-- test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");--> + <test> + <param name="bamfile" value="6_ct_replace.sam" ftype="sam" /> + <param name="tempcigar" value="-c" /> + <output name="output" file="6_ct_replace.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> + </test> + <!-- test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");--> + <test> + <param name="bamfile" value="7_two_read_mapped.sam" ftype="sam" /> + <output name="output" file="7_two_read_mapped.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> + </test> + <!--test_cmd($opts,out=>'fixmate/7_two_read_mapped.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/7_two_read_mapped.sam -");--> </tests> <help> **What it does**