# HG changeset patch
# User jjohnson
# Date 1494881071 14400
# Node ID 59f09c61031c8c629212db9032025beb3c065028
# Parent  8c17ddca0eeee85c11fdd4e0db83c8a64f2ef048
Deleted selected files

diff -r 8c17ddca0eee -r 59f09c61031c ._bamtools-split-ref.xml
Binary file ._bamtools-split-ref.xml has changed
diff -r 8c17ddca0eee -r 59f09c61031c ._bamtools-split-tag.xml
Binary file ._bamtools-split-tag.xml has changed
diff -r 8c17ddca0eee -r 59f09c61031c bamtools-split.xml.save
--- a/bamtools-split.xml.save	Mon May 15 16:27:18 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,146 +0,0 @@
-<tool id="bamSplit" name="Split" version="2.4.1">
-    <description>BAM datasets on variety of attributes</description>
-    <macros>
-        <xml name="macro_output_type">
-            <param name="output_type" type="select" label="output as">
-                <option value="history_items">history items</option>
-                <option value="dataset_collection">dataset_collection</option>
-            </param>
-        </xml>
-    </macros>
-    <requirements>
-        <requirement type="package" version="2.4.0">bamtools</requirement>
-    </requirements>
-    <command>
-        <![CDATA[
-            echo "BAM" > $report &&
-            #for $bam_count, $input_bam in enumerate( $input_bams ):
-                ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
-                ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
-            #end for
-            bamtools
-            split
-            #if str ( $analysis_type.analysis_type_selector ) == "-tag" :
-                ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}"
-            #else
-                ${analysis_type.analysis_type_selector}
-            #end if
-            -stub split_bam
-            #for $bam_count, $input_bam in enumerate( $input_bams ):
-                -in "localbam_${bam_count}.bam"
-            #end for
-            #if str ( $analysis_type.analysis_type_selector ) == "-reference"  and $analysis_type.output_type == "dataset_collection": 
-                #import re
-                #set $name = $re.sub('\W','_',$re.sub('\.bam$','',$input_bams[0].name))
-                #set $ref_list = ' '.join([$re.sub('^.*__sq__(.+)__sq__.*$','\\1',n) if n.find('__sq__') >= 0 else n for n in str($input_bam.metadata.reference_names).split(',')])
-                    && (export I=0; 
-                      for i in $ref_list; 
-                        do I=\$((++I)); SN=`printf "split_bam.REF_%s.bam" "\$i"`; 
-                           if [ -e \$SN ]; 
-                             then FN=`printf "split_bam%05d%s.%s.bam" \$((I)) "$name" "\$i"`; 
-                             mv \$SN \$FN;
-                           fi;
-                        done)
-            #end if
-        ]]>
-    </command>
-    <inputs>
-        <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
-        <conditional name="analysis_type">
-            <param name="analysis_type_selector" type="select" label="Split BAM dataset(s) by" help="See help below for explanation of each option">
-                <option value="-mapped">Mapping status (-mapped)</option>
-                <option value="-paired">Pairing status (-paired)</option>
-                <option value="-reference">Reference name (-reference)</option>
-                <option value="-tag">Specific tag (-tag)</option>
-            </param>
-            <when value="-mapped" />
-            <when value="-paired" />
-            <when value="-reference" >
-                <expand macro="macro_output_type" />
-            </when>
-            <when value="-tag">
-                <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter &quot;NM&quot;"/>
-                <expand macro="macro_output_type" />
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data format="txt" name="report" label="BAMSplitter Run" hidden="true">
-            <discover_datasets pattern="split_bam\.(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true"/>
-            <filter>analysis_type['analysis_type_selector'] in ('-mapped','-paired') or analysis_type['output_type'] != 'dataset_collection'</filter>
-        </data>
-        <collection name="output_bams" type="list" label="${input_bams[0].name} by ${analysis_type.analysis_type_selector.replace('-','')}">
-            <discover_datasets pattern="split_bam\d*(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="false"/>
-            <filter>analysis_type['analysis_type_selector'] in ('-reference','-tag') and analysis_type['output_type'] == 'dataset_collection'</filter>
-        </collection>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
-            <param name="analysis_type_selector" value="-mapped"/>
-            <output name="report">
-                <assert_contents>
-                    <has_line line="BAM" />
-                </assert_contents>
-                <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/>
-            </output>
-        </test>
-        <test>
-            <param name="input_bams" ftype="bam" value="bamtools-input2.bam"/>
-            <param name="analysis_type_selector" value="-reference"/>
-            <param name="output_type" value="dataset_collection"/>
-            <output_collection name="output_bams"  type="list">
-                <element name="bamtools_input2.chr1"  file="bamtools_input2.chr1" compare="sim_size" delta="500" />
-            </output_collection>
-        </test>
-
-    </tests>
-    <help>
-**What is does**
-
-BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
-
------
-
-.. class:: warningmark
-
-**DANGER: Multiple Outputs**
-
-As described below, splitting a BAM dataset(s) on reference name or a tag value can produce very large numbers of outputs. Read below and know what you are doing.
-
------
-
-**How it works**
-
-The following options can be specified via "**Split BAM dataset(s) by**" dropdown::
-
-  Mapping status (-mapped)          split mapped/unmapped and generate two output files
-                                    named (MAPPED) and (UNMAPPED) containing mapped and unmapped
-                                    reads, respectively.
-
-  Pairing status (-paired)          split single-end/paired-end alignments and generate two output files
-                                    named (SINGLE_END) and (PAIRED_END) containing paired and unpaired
-                                    reads, respectively.
-
-  Reference name (-reference)       split alignments by reference name. In cases of unfinished genomes with
-                                    very large number of reference sequences (scaffolds) it can generate
-                                    thousands (if not millions) of output datasets.
-
-  Specific tag (-tag)               split alignments based on all values of TAG encountered. Choosing this
-                                    option from the menu will allow you to enter the tag name. As was the
-                                    case with the reference splitting above, this option can produce very
-                                    large number of outputs if a tag has a large number of unique values.
-
------
-
-.. class:: infomark
-
-**More information**
-
-Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
-
-    </help>
-    <citations>
-        <citation type="doi">10.1093/bioinformatics/btr174</citation>
-    </citations>
-</tool>