# HG changeset patch
# User iuc
# Date 1528324995 14400
# Node ID 3263a2b5d9f0be82022a2646e07efb0d16e2f347
# Parent  1609642558887628b313c7a848f2e0b740e38d25
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e

diff -r 160964255888 -r 3263a2b5d9f0 samtool_filter2.xml
--- a/samtool_filter2.xml	Thu Oct 05 10:31:25 2017 -0400
+++ b/samtool_filter2.xml	Wed Jun 06 18:43:15 2018 -0400
@@ -1,182 +1,175 @@
-<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.2">
-  <description>files on FLAG MAPQ RG LN or by region</description>
-  <requirements>
-    <requirement type="package" version="1.2">samtools</requirement>
-  </requirements>
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
-  <command>
-<![CDATA[
+<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.8">
+    <description>files on FLAG MAPQ RG LN or by region</description>
+    <requirements>
+        <requirement type="package" version="1.8">samtools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
 ##set up input files, regions requires input.bam and input.bai
 #if $input1.is_of_type('bam')
-  #set $input = 'input.bam'
-  ln -s '$input1' $input &&
-  ln -s '$input1.metadata.bam_index' input.bai &&
+    #set $input = 'input.bam'
+    ln -s '$input1' $input &&
+    ln -s '$input1.metadata.bam_index' input.bai &&
 #elif $input1.is_of_type('sam')
-  #set $input = 'input.sam'
-  ln -s '$input1' $input &&
+    #set $input = 'input.sam'
+    ln -s '$input1' $input &&
 #end if
-samtools view $possibly_select_inverse '$output1' $header
+samtools view
+$possibly_select_inverse '$output1'
+$header
 
-  #if $input1.is_of_type('sam')
+#if $input1.is_of_type('sam')
    -S
-  #end if
+#end if
 
-  #if str($outputtype) == 'bam'
-      -b
-  #end if
+#if str($outputtype) == 'bam'
+    -b
+#end if
 
-  #if str($mapq)
-   -q $mapq
-  #end if
-  #if $flag.filter == 'yes'
-   #if str($flag.reqBits) != 'None'
-     #set $reqs = str($flag.reqBits).split(',')
-     #set $reqFlag = 0
-     #for $xn in $reqs:
-       #set $reqFlag += int($xn, 16)
-     #end for
-     -f $hex($reqFlag)
-   #end if
-   #if str($flag.skipBits) != 'None'
-     #set $skips = str($flag.skipBits).split(',')
-     #set $skipFlag = 0
-     #for $xn in $skips:
-       #set $skipFlag += int(xn,16)
-     #end for
-     -F $hex($skipFlag)
-   #end if
-  #end if
-  #if str($read_group).strip()
+#if str($mapq)
+    -q $mapq
+#end if
+#if $flag.filter == 'yes'
+    #if str($flag.reqBits) != 'None'
+        #set $reqs = str($flag.reqBits).split(',')
+        #set $reqFlag = 0
+        #for $xn in $reqs:
+            #set $reqFlag += int($xn, 16)
+        #end for
+        -f $hex($reqFlag)
+    #end if
+    #if str($flag.skipBits) != 'None'
+        #set $skips = str($flag.skipBits).split(',')
+        #set $skipFlag = 0
+        #for $xn in $skips:
+            #set $skipFlag += int(xn,16)
+        #end for
+        -F $hex($skipFlag)
+    #end if
+#end if
+#if str($read_group).strip()
     -r '$read_group'
-  #end if
-  #if str($library).strip()
+#end if
+#if str($library).strip()
     -l '$library'
-  #end if
-  #if $bed_file
+#end if
+#if $bed_file
     -L '$bed_file'
-  #end if
-  $input
-  #if str($regions).strip() and $input1.is_of_type('bam')
+#end if
+$input
+#if str($regions).strip() and $input1.is_of_type('bam')
     #for region in str($regions).split():
-      '$region'
+        '$region'
     #end for
-  #end if
-  ## need to redirect stderr message so galaxy does not think this failed
-  2>&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" help="(-q)">
-      <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" 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>
-          <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>
-          <option value="0x0800">Supplementary alignment</option>
-        </param>
-        <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>
-          <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>
-          <option value="0x0800">Supplementary alignment</option>
+#end if
+    ]]></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>
-      </when>
-    </conditional>
-    <param name="library" type="text" value="" label="Select alignments from Library"
-           help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
-    <param name="read_group" type="text" value="" 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="possibly_select_inverse" checked="false" label="Use inverse selection" type="boolean" truevalue="-U" falsevalue="-o" help="Select the opposite of the listed chromosomes" />
-    <param name="regions" type="text" value="" 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 (-b)</option>
-        <option value="sam">SAM</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="output1" format="sam" label="${tool.name} on ${on_string}: ${outputtype}">
-      <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"/>
-      <param name="outputtype" value="sam"/>
-      <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"/>
-      <param name="outputtype" value="sam"/>
-      <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"/>
-      <param name="outputtype" value="sam"/>
-      <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>
+        <param name="mapq" type="integer" min="0" value="" optional="true" label="Minimum MAPQ quality score" help="(-q)" />
+        <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" 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>
+                    <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>
+                    <option value="0x0800">Supplementary alignment</option>
+                </param>
+                <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>
+                    <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>
+                    <option value="0x0800">Supplementary alignment</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="library" type="text" value="" label="Select alignments from Library"
+            help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
+        <param name="read_group" type="text" value="" 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="possibly_select_inverse" type="boolean" truevalue="-U" falsevalue="-o" checked="false" label="Use inverse selection" help="Select the opposite of the listed chromosomes" />
+        <param name="regions" type="text" value="" 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 (-b)</option>
+            <option value="sam">SAM</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output1" format="sam" label="${tool.name} on ${on_string}: ${outputtype}">
+            <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"/>
+            <param name="outputtype" value="sam"/>
+            <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"/>
+            <param name="outputtype" value="sam"/>
+            <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"/>
+            <param name="outputtype" value="sam"/>
+            <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><![CDATA[
 **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.
@@ -206,9 +199,9 @@
 
   chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX
 
-
-
 .. _SAMtools: http://www.htslib.org/
-
-  </help>
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp352</citation>
+    </citations>
 </tool>
diff -r 160964255888 -r 3263a2b5d9f0 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Oct 05 10:31:25 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="samtools" version="1.2">
-    <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-  </package>
-</tool_dependency>