| Previous changeset 0:2d4ae2f8231e (2014-02-27) Next changeset 2:886b73f04847 (2015-10-09) |
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Commit message:
planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 |
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modified:
samtool_filter2.xml tool_dependencies.xml |
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| diff -r 2d4ae2f8231e -r 94d5786febc4 samtool_filter2.xml --- a/samtool_filter2.xml Thu Feb 27 16:16:26 2014 -0500 +++ b/samtool_filter2.xml Mon Aug 10 17:14:37 2015 -0400 |
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| b'@@ -3,58 +3,36 @@\n <requirements>\n <requirement type="package" version="0.1.18">samtools</requirement>\n </requirements>\n- <!-- \n- samtools view [-bchuHS] [-t in.refList] [-o output] [-f reqFlag] [-F skipFlag] [-q minMapQ] [-l library] [-r readGroup] [-R rgFile] <in.bam>|<in.sam> [region1 [...]]\n- Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]\n-\n- Options: -b output BAM\n- -h print header for the SAM output\n- -H print header only (no alignments)\n- -S input is SAM\n- -u uncompressed BAM output (force -b)\n- -1 fast compression (force -b)\n- -x output FLAG in HEX (samtools-C specific)\n- -X output FLAG in string (samtools-C specific)\n- -c print only the count of matching records\n- -L FILE output alignments overlapping the input BED FILE [null]\n- -t FILE list of reference names and lengths (force -S) [null]\n- -T FILE reference sequence file (force -S) [null]\n- -o FILE output file name [stdout]\n- -R FILE list of read groups to be outputted [null]\n- -f INT required flag, 0 for unset [0]\n- -F INT filtering flag, 0 for unset [0]\n- -q INT minimum mapping quality [0]\n- -l STR only output reads in library STR [null]\n- -r STR only output reads in read group STR [null]\n- -? longer help\n- -->\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n <command>\n+<![CDATA[\n ##set up input files, regions requires input.bam and input.bai\n #if isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension(\'bam\').__class__):\n #set $input = \'input.bam\'\n- ln -s $input1 $input &&\n- ln -s $input1.metadata.bam_index input.bai &&\n+ ln -s "$input1" $input &&\n+ ln -s "$input1.metadata.bam_index" input.bai &&\n #elif isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension(\'sam\').__class__):\n #set $input = \'input.sam\'\n- ln -s $input1 $input &&\n+ ln -s "$input1" $input &&\n #end if\n samtools view -o "$output1" $header\n- \n+\n #if $input1.datatype.file_ext == \'sam\':\n -S\n #end if\n \n #if $outputtype.__str__ == "bam":\n- -b \n+ -b\n #end if\n- \n- \n+\n #if $mapq.__str__ != \'\':\n -q $mapq\n #end if\n #if $flag.filter.__str__ == \'yes\':\n #if $flag.reqBits.__str__ != \'None\':\n- #set $reqs = $flag.reqBits.__str__.split(\',\') \n+ #set $reqs = $flag.reqBits.__str__.split(\',\')\n #set $reqFlag = 0\n #for $xn in $reqs:\n #set $reqFlag += int(xn,16)\n@@ -62,7 +40,7 @@\n -f $hex($reqFlag)\n #end if\n #if $flag.skipBits.__str__ != \'None\':\n- #set $skips = $flag.skipBits.__str__.split(\',\') \n+ #set $skips = $flag.skipBits.__str__.split(\',\')\n #set $skipFlag = 0\n #for $xn in $skips:\n #set $skipFlag += int(xn,16)\n@@ -77,23 +55,24 @@\n -l $library\n #end if\n #if $bed_file.__str__ != "None" and len($bed_file.__str__) > 0:\n- -L $bed_file\n+ -L "$bed_file"\n #end if\n $input\n #if $regions.__str__.strip() != \'\' and $input1.datatype.file_ext == \'bam\':\n $regions.__str__.strip()\n #end if\n ## need to redirect stderr message so galaxy does not think this failed\n- 2>&1\n+ 2>&1\n+]]>\n </command>\n <inputs>\n- <param name="input1" type="data" format="sam,bam" label="SAM or BAM File to Filter" />\n+ <param name="input1" type="data" format="sam,bam" label="SAM or BAM file to filter" />\n <param name="header" type="select" label="Header in output">\n <option value="-h">Include Header</option>\n <option value="">Exclude Header</option>\n <option value="-H">Only the Header</option>\n </param>\n- <param name="mapq" type="integer" value="" optional="true" label="Minimum MAPQ quality score">\n+ <param name="mapq" type="integer" value="" o'..b'="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE" help="(-L)"/>\n+ <param name="regions" type="text" value="" size="180" label="Select regions (only used when the input is in BAM format)"\n help="region should be presented in one of the following formats: `chr1\', `chr2:1,000\' and `chr3:1000-2,000\'"/>\n <param name="outputtype" type="select" label="Select the output format">\n- <option value="bam">bam</option>\n- <option value="sam">sam</option>\n+ <option value="bam">BAM (-b)</option>\n+ <option value="sam">SAM</option>\n </param>\n </inputs>\n <outputs>\n- <data name="output1" format_source="input1" label="${tool.name} on ${on_string}: ${input1.datatype.file_ext}">\n+ <data name="output1" format="sam" label="${tool.name} on ${on_string}: ${outputtype}">\n <change_format>\n <when input="outputtype" value="bam" format="bam" />\n </change_format>\n@@ -157,11 +136,11 @@\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+ <output name="output1">\n+ <assert_contents>\n+ <has_text text="141" />\n <not_has_text text="77" />\n- </assert_contents> \n+ </assert_contents>\n </output>\n </test>\n <test>\n@@ -170,11 +149,11 @@\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+ <output name="output1">\n+ <assert_contents>\n+ <has_text text="rg1" />\n <not_has_text text="rg2" />\n- </assert_contents> \n+ </assert_contents>\n </output>\n </test>\n <test>\n@@ -184,20 +163,18 @@\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+ <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+ </assert_contents>\n </output>\n </test>\n </tests>\n <help>\n- \n-\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+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 \n **Input**\n \n@@ -209,14 +186,14 @@\n \n **Options**\n \n-Filtering by read group or library requires headers in the input SAM or BAM file. \n+Filtering by read group or library requires headers in the input SAM or BAM file.\n \n-If regions are specified, only alignments overlapping the specified regions will be output. An alignment may be given multiple times if it is overlapping several regions. \n+If regions are specified, only alignments overlapping the specified regions will be output. An alignment may be given multiple times if it is overlapping several regions.\n A region can be presented, for example, in the following format::\n \n chr2\t(the whole chr2)\n- chr2:1000000\t (region starting from 1,000,000bp) \n- chr2:1,000,000-2,000,000\t(region between 1,000,000 and 2,000,000bp including the end points). \n+ chr2:1000000\t (region starting from 1,000,000bp)\n+ chr2:1,000,000-2,000,000\t(region between 1,000,000 and 2,000,000bp including the end points).\n \n Note: The coordinate is 1-based.\n \n@@ -226,7 +203,7 @@\n \n \n \n-.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml\n+.. _SAMtools: http://samtools.sourceforge.net/\n \n </help>\n </tool>\n' |
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| diff -r 2d4ae2f8231e -r 94d5786febc4 tool_dependencies.xml --- a/tool_dependencies.xml Thu Feb 27 16:16:26 2014 -0500 +++ b/tool_dependencies.xml Mon Aug 10 17:14:37 2015 -0400 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.18"> - <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |