Mercurial > repos > devteam > samtool_filter2
diff samtool_filter2.xml @ 1:94d5786febc4 draft
planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062
| author | devteam |
|---|---|
| date | Mon, 10 Aug 2015 17:14:37 -0400 |
| parents | 2d4ae2f8231e |
| children | 886b73f04847 |
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--- a/samtool_filter2.xml Thu Feb 27 16:16:26 2014 -0500 +++ b/samtool_filter2.xml Mon Aug 10 17:14:37 2015 -0400 @@ -3,58 +3,36 @@ <requirements> <requirement type="package" version="0.1.18">samtools</requirement> </requirements> - <!-- - 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 [...]] - Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]] - - Options: -b output BAM - -h print header for the SAM output - -H print header only (no alignments) - -S input is SAM - -u uncompressed BAM output (force -b) - -1 fast compression (force -b) - -x output FLAG in HEX (samtools-C specific) - -X output FLAG in string (samtools-C specific) - -c print only the count of matching records - -L FILE output alignments overlapping the input BED FILE [null] - -t FILE list of reference names and lengths (force -S) [null] - -T FILE reference sequence file (force -S) [null] - -o FILE output file name [stdout] - -R FILE list of read groups to be outputted [null] - -f INT required flag, 0 for unset [0] - -F INT filtering flag, 0 for unset [0] - -q INT minimum mapping quality [0] - -l STR only output reads in library STR [null] - -r STR only output reads in read group STR [null] - -? longer help - --> + <stdio> + <exit_code range="1:" /> + </stdio> <command> +<![CDATA[ ##set up input files, regions requires input.bam and input.bai #if isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('bam').__class__): #set $input = 'input.bam' - ln -s $input1 $input && - ln -s $input1.metadata.bam_index input.bai && + ln -s "$input1" $input && + ln -s "$input1.metadata.bam_index" input.bai && #elif isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sam').__class__): #set $input = 'input.sam' - ln -s $input1 $input && + ln -s "$input1" $input && #end if samtools view -o "$output1" $header - + #if $input1.datatype.file_ext == 'sam': -S #end if #if $outputtype.__str__ == "bam": - -b + -b #end if - - + #if $mapq.__str__ != '': -q $mapq #end if #if $flag.filter.__str__ == 'yes': #if $flag.reqBits.__str__ != 'None': - #set $reqs = $flag.reqBits.__str__.split(',') + #set $reqs = $flag.reqBits.__str__.split(',') #set $reqFlag = 0 #for $xn in $reqs: #set $reqFlag += int(xn,16) @@ -62,7 +40,7 @@ -f $hex($reqFlag) #end if #if $flag.skipBits.__str__ != 'None': - #set $skips = $flag.skipBits.__str__.split(',') + #set $skips = $flag.skipBits.__str__.split(',') #set $skipFlag = 0 #for $xn in $skips: #set $skipFlag += int(xn,16) @@ -77,23 +55,24 @@ -l $library #end if #if $bed_file.__str__ != "None" and len($bed_file.__str__) > 0: - -L $bed_file + -L "$bed_file" #end if $input #if $regions.__str__.strip() != '' and $input1.datatype.file_ext == 'bam': $regions.__str__.strip() #end if ## need to redirect stderr message so galaxy does not think this failed - 2>&1 + 2>&1 +]]> </command> <inputs> - <param name="input1" type="data" format="sam,bam" label="SAM or BAM File to Filter" /> + <param name="input1" type="data" format="sam,bam" label="SAM or BAM file to filter" /> <param name="header" type="select" label="Header in output"> <option value="-h">Include Header</option> <option value="">Exclude Header</option> <option value="-H">Only the Header</option> </param> - <param name="mapq" type="integer" value="" optional="true" label="Minimum MAPQ quality score"> + <param name="mapq" type="integer" value="" optional="true" label="Minimum MAPQ quality score" help="(-q)"> <validator type="in_range" message="The MAPQ quality score can't be negative" min="0"/> </param> <conditional name="flag"> @@ -103,7 +82,7 @@ </param> <when value="no"/> <when value="yes"> - <param name="reqBits" type="select" multiple="true" display="checkboxes" label="Only output alignments with all of these flag bits set" > + <param name="reqBits" type="select" multiple="true" display="checkboxes" label="Only output alignments with all of these flag bits set" help="(-f)"> <option value="0x0001">Read is paired</option> <option value="0x0002">Read is mapped in a proper pair</option> <option value="0x0004">The read is unmapped</option> @@ -116,7 +95,7 @@ <option value="0x0200">The read fails platform/vendor quality checks</option> <option value="0x0400">The read is a PCR or optical duplicate</option> </param> - <param name="skipBits" type="select" multiple="true" display="checkboxes" label="Skip alignments with any of these flag bits set" > + <param name="skipBits" type="select" multiple="true" display="checkboxes" label="Skip alignments with any of these flag bits set" help="(-F)"> <option value="0x0001">Read is paired</option> <option value="0x0002">Read is mapped in a proper pair</option> <option value="0x0004">The read is unmapped</option> @@ -132,19 +111,19 @@ </when> </conditional> <param name="library" type="text" value="" size="20" label="Select alignments from Library" - help="Requires headers in the input SAM or BAM, otherwise no alignments will be output."/> - <param name="read_group" type="text" value="" size="20" label="Select alignments from Read Group" - help="Requires headers in the input SAM or BAM, otherwise no alignments will be output."/> - <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE"/> - <param name="regions" type="text" value="" size="180" label="Select regions (only used when the input is in BAM format)" + help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/> + <param name="read_group" type="text" value="" size="20" label="Select alignments from Read Group" + help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/> + <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE" help="(-L)"/> + <param name="regions" type="text" value="" size="180" label="Select regions (only used when the input is in BAM format)" help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/> <param name="outputtype" type="select" label="Select the output format"> - <option value="bam">bam</option> - <option value="sam">sam</option> + <option value="bam">BAM (-b)</option> + <option value="sam">SAM</option> </param> </inputs> <outputs> - <data name="output1" format_source="input1" label="${tool.name} on ${on_string}: ${input1.datatype.file_ext}"> + <data name="output1" format="sam" label="${tool.name} on ${on_string}: ${outputtype}"> <change_format> <when input="outputtype" value="bam" format="bam" /> </change_format> @@ -157,11 +136,11 @@ <param name="filter" value="yes"/> <param name="reqBits" value="0x0080"/> <param name="outputtype" value="sam"/> - <output name="output1" > - <assert_contents> - <has_text text="141" /> + <output name="output1"> + <assert_contents> + <has_text text="141" /> <not_has_text text="77" /> - </assert_contents> + </assert_contents> </output> </test> <test> @@ -170,11 +149,11 @@ <param name="filter" value="no"/> <param name="read_group" value="rg1"/> <param name="outputtype" value="sam"/> - <output name="output1" > - <assert_contents> - <has_text text="rg1" /> + <output name="output1"> + <assert_contents> + <has_text text="rg1" /> <not_has_text text="rg2" /> - </assert_contents> + </assert_contents> </output> </test> <test> @@ -184,20 +163,18 @@ <param name="skipBits" value="0x0008"/> <param name="mapq" value="250"/> <param name="outputtype" value="sam"/> - <output name="output1" > - <assert_contents> - <has_text text="both_reads_align_clip_marked" /> + <output name="output1"> + <assert_contents> + <has_text text="both_reads_align_clip_marked" /> <not_has_text text="both_reads_present_only_first_aligns" /> - </assert_contents> + </assert_contents> </output> </test> </tests> <help> - - **What it does** -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. +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. **Input** @@ -209,14 +186,14 @@ **Options** -Filtering by read group or library requires headers in the input SAM or BAM file. +Filtering by read group or library requires headers in the input SAM or BAM file. -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. +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. A region can be presented, for example, in the following format:: chr2 (the whole chr2) - chr2:1000000 (region starting from 1,000,000bp) - chr2:1,000,000-2,000,000 (region between 1,000,000 and 2,000,000bp including the end points). + chr2:1000000 (region starting from 1,000,000bp) + chr2:1,000,000-2,000,000 (region between 1,000,000 and 2,000,000bp including the end points). Note: The coordinate is 1-based. @@ -226,7 +203,7 @@ -.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml +.. _SAMtools: http://samtools.sourceforge.net/ </help> </tool>