# HG changeset patch
# User devteam
# Date 1385574137 18000
# Node ID 8ee90c5631c7bcb9dca4ae57a88a7297898133f4
# Parent  f964ba4c93bc8b6ef6df1f956a1bdfed02ef1d75
Deleted selected files

diff -r f964ba4c93bc -r 8ee90c5631c7 samtools_filter.xml
--- a/samtools_filter.xml	Tue Nov 26 14:18:37 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,229 +0,0 @@
-<tool id="samtools_filter" name="Filter SAM or BAM" version="1.1.1">
-  <description>files on FLAG MAPQ RG LN or by region</description>
-  <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
-  -->
-  <command>
-##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  &amp;&amp;
-  ln -s $input1.metadata.bam_index input.bai  &amp;&amp;
-#elif isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sam').__class__):
-  #set $input = 'input.sam'
-  ln -s $input1 $input  &amp;&amp;
-#end if
-samtools view -o "$output1" $header
-  
-  #if $input1.datatype.file_ext == 'sam':
-   -S
-  #end if
-
-  #if $outputtype.__str__ == "bam":
-      -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 $reqFlag = 0
-     #for $xn in $reqs:
-       #set $reqFlag += int(xn,16)
-     #end for
-     -f $hex($reqFlag)
-   #end if
-   #if $flag.skipBits.__str__ != 'None':
-     #set $skips = $flag.skipBits.__str__.split(',') 
-     #set $skipFlag = 0
-     #for $xn in $skips:
-       #set $skipFlag += int(xn,16)
-     #end for
-     -F $hex($skipFlag)
-   #end if
-  #end if
-  #if $read_group.__str__.strip() != '':
-    -r $read_group
-  #end if
-  #if $library.__str__.strip() != '':
-    -l $library
-  #end if
-  #if $bed_file.__str__ != "None" and len($bed_file.__str__) > 0:
-    -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>&amp;1
-  </command>
-  <inputs>
-    <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">
-      <validator type="in_range" message="The MAPQ quality score can't be negative" min="0"/>
-    </param>
-    <conditional name="flag">
-      <param name="filter" type="select" label="Filter on bitwise flag">
-        <option value="no">no</option>
-        <option value="yes">yes</option>
-      </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" >
-          <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>
-          <option value="0x0008">The mate is unmapped</option>
-          <option value="0x0010">Read strand</option>
-          <option value="0x0020">Mate strand</option>
-          <option value="0x0040">Read is the first in a pair</option>
-          <option value="0x0080">Read is the second in a pair</option>
-          <option value="0x0100">The alignment or this read is not primary</option>
-          <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" >
-          <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>
-          <option value="0x0008">The mate is unmapped</option>
-          <option value="0x0010">Read strand</option>
-          <option value="0x0020">Mate strand</option>
-          <option value="0x0040">Read is the first in a pair</option>
-          <option value="0x0080">Read is the second in a pair</option>
-          <option value="0x0100">The alignment or this read is not primary</option>
-          <option value="0x0200">The read fails platform/vendor quality checks</option>
-          <option value="0x0400">The read is a PCR or optical duplicate</option>
-        </param>
-      </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="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>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="output1" format_source="input1" label="${tool.name} on ${on_string}: ${input1.datatype.file_ext}">
-      <change_format>
-        <when input="outputtype" value="bam" format="bam" />
-      </change_format>
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />
-      <param name="header" value=""/>
-      <param name="filter" value="yes"/>
-      <param name="reqBits" value="0x0080"/>
-      <output name="output1" >
-       <assert_contents> 
-         <has_text text="141" /> 
-         <not_has_text text="77" />
-       </assert_contents> 
-      </output>
-    </test>
-    <test>
-      <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />
-      <param name="header" value=""/>
-      <param name="filter" value="no"/>
-      <param name="read_group" value="rg1"/>
-      <output name="output1" >
-       <assert_contents> 
-         <has_text text="rg1" /> 
-         <not_has_text text="rg2" />
-       </assert_contents> 
-      </output>
-    </test>
-    <test>
-      <param name="input1" value="bam_to_sam_in1.sam" ftype="sam" />
-      <param name="header" value=""/>
-      <param name="filter" value="yes"/>
-      <param name="skipBits" value="0x0008"/>
-      <param name="mapq" value="250"/>
-      <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> 
-      </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.
-
-**Input**
-
-Input is either a SAM or BAM file.
-
-**Output**
-
-The output file will be SAM or BAM (depending on the chosen option), filtered by the selected options.
-
-**Options**
-
-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.  
-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). 
-
-Note:  The coordinate is 1-based.
-
-Multiple regions may be specified, separated by a space character::
-
-  chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX
-
-
-
-.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
-
-  </help>
-</tool>