| Previous changeset 6:dc6ff68ea5e8 (2017-10-05) Next changeset 8:a7add3e93cc5 (2019-07-31) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e |
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modified:
samtool_filter2.xml |
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removed:
tool_dependencies.xml |
| b |
| diff -r dc6ff68ea5e8 -r 56c31114ad4a samtool_filter2.xml --- a/samtool_filter2.xml Thu Oct 05 10:31:42 2017 -0400 +++ b/samtool_filter2.xml Wed Jun 06 18:43:29 2018 -0400 |
| [ |
| b'@@ -1,182 +1,175 @@\n-<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.2">\n- <description>files on FLAG MAPQ RG LN or by region</description>\n- <requirements>\n- <requirement type="package" version="1.2">samtools</requirement>\n- </requirements>\n- <stdio>\n- <exit_code range="1:" />\n- </stdio>\n- <command>\n-<![CDATA[\n+<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.8">\n+ <description>files on FLAG MAPQ RG LN or by region</description>\n+ <requirements>\n+ <requirement type="package" version="1.8">samtools</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n ##set up input files, regions requires input.bam and input.bai\n #if $input1.is_of_type(\'bam\')\n- #set $input = \'input.bam\'\n- ln -s \'$input1\' $input &&\n- ln -s \'$input1.metadata.bam_index\' input.bai &&\n+ #set $input = \'input.bam\'\n+ ln -s \'$input1\' $input &&\n+ ln -s \'$input1.metadata.bam_index\' input.bai &&\n #elif $input1.is_of_type(\'sam\')\n- #set $input = \'input.sam\'\n- ln -s \'$input1\' $input &&\n+ #set $input = \'input.sam\'\n+ ln -s \'$input1\' $input &&\n #end if\n-samtools view $possibly_select_inverse \'$output1\' $header\n+samtools view\n+$possibly_select_inverse \'$output1\'\n+$header\n \n- #if $input1.is_of_type(\'sam\')\n+#if $input1.is_of_type(\'sam\')\n -S\n- #end if\n+#end if\n \n- #if str($outputtype) == \'bam\'\n- -b\n- #end if\n+#if str($outputtype) == \'bam\'\n+ -b\n+#end if\n \n- #if str($mapq)\n- -q $mapq\n- #end if\n- #if $flag.filter == \'yes\'\n- #if str($flag.reqBits) != \'None\'\n- #set $reqs = str($flag.reqBits).split(\',\')\n- #set $reqFlag = 0\n- #for $xn in $reqs:\n- #set $reqFlag += int($xn, 16)\n- #end for\n- -f $hex($reqFlag)\n- #end if\n- #if str($flag.skipBits) != \'None\'\n- #set $skips = str($flag.skipBits).split(\',\')\n- #set $skipFlag = 0\n- #for $xn in $skips:\n- #set $skipFlag += int(xn,16)\n- #end for\n- -F $hex($skipFlag)\n- #end if\n- #end if\n- #if str($read_group).strip()\n+#if str($mapq)\n+ -q $mapq\n+#end if\n+#if $flag.filter == \'yes\'\n+ #if str($flag.reqBits) != \'None\'\n+ #set $reqs = str($flag.reqBits).split(\',\')\n+ #set $reqFlag = 0\n+ #for $xn in $reqs:\n+ #set $reqFlag += int($xn, 16)\n+ #end for\n+ -f $hex($reqFlag)\n+ #end if\n+ #if str($flag.skipBits) != \'None\'\n+ #set $skips = str($flag.skipBits).split(\',\')\n+ #set $skipFlag = 0\n+ #for $xn in $skips:\n+ #set $skipFlag += int(xn,16)\n+ #end for\n+ -F $hex($skipFlag)\n+ #end if\n+#end if\n+#if str($read_group).strip()\n -r \'$read_group\'\n- #end if\n- #if str($library).strip()\n+#end if\n+#if str($library).strip()\n -l \'$library\'\n- #end if\n- #if $bed_file\n+#end if\n+#if $bed_file\n -L \'$bed_file\'\n- #end if\n- $input\n- #if str($regions).strip() and $input1.is_of_type(\'bam\')\n+#end if\n+$input\n+#if str($regions).strip() and $input1.is_of_type(\'bam\')\n #for region in str($regions).split():\n- \'$region\'\n+ \'$region\'\n #end for\n- #end if\n- ## need to redirect stderr message so galaxy does not think this failed\n- 2>&1\n-]]>\n- </command>\n- <inputs>\n- <param name="input1" type="data" format="sam,bam" label="SAM or BAM file to filter" />\n- <param name="header" type="select" label="Header in output">\n- <option value="-h">Include Header</option>\n- <option value="">Exclude Header</option>\n- <option value="-H">Only the Header</option>\n- </param>\n- <param name="mapq" type="integer" value="" optional="true" label="Minimum MAPQ quality score" help="(-q)">\n- <validator type="in_range" message="The MAPQ quality score can\'t be negative" min="0"/>\n- </param>\n- <conditional name="flag">\n- <param name="filter" type="select" label="Filter on bitwise flag">\n- <option value="no">no</option>\n- <option value="yes">yes</option>\n- </param>\n- <when value="no"/>\n- <when va'..b' <option value="0x0200">The read fails platform/vendor quality checks</option>\n+ <option value="0x0400">The read is a PCR or optical duplicate</option>\n+ <option value="0x0800">Supplementary alignment</option>\n+ </param>\n+ </when>\n+ </conditional>\n+ <param name="library" type="text" value="" label="Select alignments from Library"\n+ help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>\n+ <param name="read_group" type="text" value="" label="Select alignments from Read Group"\n+ help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>\n+ <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED file" help="(-L)"/>\n+ <param name="possibly_select_inverse" type="boolean" truevalue="-U" falsevalue="-o" checked="false" label="Use inverse selection" help="Select the opposite of the listed chromosomes" />\n+ <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)"\n+ help="region should be presented in one of the following formats: `chr1\', `chr2:1,000\' and `chr3:1000-2,000\'"/>\n+ <param name="outputtype" type="select" label="Select the output format">\n+ <option value="bam">BAM (-b)</option>\n+ <option value="sam">SAM</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data name="output1" format="sam" label="${tool.name} on ${on_string}: ${outputtype}">\n+ <change_format>\n+ <when input="outputtype" value="bam" format="bam" />\n+ </change_format>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />\n+ <param name="header" value=""/>\n+ <param name="filter" value="yes"/>\n+ <param name="reqBits" value="0x0080"/>\n+ <param name="outputtype" value="sam"/>\n+ <output name="output1">\n+ <assert_contents>\n+ <has_text text="141" />\n+ <not_has_text text="77" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />\n+ <param name="header" value=""/>\n+ <param name="filter" value="no"/>\n+ <param name="read_group" value="rg1"/>\n+ <param name="outputtype" value="sam"/>\n+ <output name="output1">\n+ <assert_contents>\n+ <has_text text="rg1" />\n+ <not_has_text text="rg2" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input1" value="bam_to_sam_in1.sam" ftype="sam" />\n+ <param name="header" value=""/>\n+ <param name="filter" value="yes"/>\n+ <param name="skipBits" value="0x0008"/>\n+ <param name="mapq" value="250"/>\n+ <param name="outputtype" value="sam"/>\n+ <output name="output1">\n+ <assert_contents>\n+ <has_text text="both_reads_align_clip_marked" />\n+ <not_has_text text="both_reads_present_only_first_aligns" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n **What it does**\n \n This tool uses the samtools view command in SAMtools_ toolkit to filter a SAM or BAM file on the MAPQ (mapping quality), FLAG bits, Read Group, Library, or region.\n@@ -206,9 +199,9 @@\n \n chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX\n \n-\n-\n .. _SAMtools: http://www.htslib.org/\n-\n- </help>\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btp352</citation>\n+ </citations>\n </tool>\n' |
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| diff -r dc6ff68ea5e8 -r 56c31114ad4a tool_dependencies.xml --- a/tool_dependencies.xml Thu Oct 05 10:31:42 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="samtools" version="1.2"> - <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |