# HG changeset patch
# User iuc
# Date 1673444471 0
# Node ID 20ad2e231693121f5e21ed550ab949a0032ecfef
# Parent  9dbf707bebb0323cd1f0e91d8d65944fdbeabeda
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty

diff -r 9dbf707bebb0 -r 20ad2e231693 bamtools_split.xml
--- a/bamtools_split.xml	Wed Jan 11 12:03:53 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,119 +0,0 @@
-<tool id="bamtools_split" name="Split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>BAM datasets on variety of attributes</description>
-    <macros>
-          <import>macros.xml</import>
-    </macros>
-    <expand macro="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
-        ]]>
-    </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" />
-            <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;"/>
-            </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"/>
-        </data>
-    </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"/>
-            <output name="report">
-                <assert_contents>
-                    <has_line line="BAM" />
-                </assert_contents>
-                <discovered_dataset designation="REF_chr1" file="bamtools_input2.chr1" ftype="bam"/>
-            </output>
-        </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>
diff -r 9dbf707bebb0 -r 20ad2e231693 bamtools_split_mapped.xml
--- a/bamtools_split_mapped.xml	Wed Jan 11 12:03:53 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-<tool id="bamtools_split_mapped" name="Split BAM by Mapped" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description></description>
-    <macros>
-          <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <command>
-        <![CDATA[
-            ln -s '${input_bam}' 'localbam.bam' &&
-            ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' &&
-            bamtools split -mapped
-            -in localbam.bam
-            -stub split_bam
-        ]]>
-    </command>
-    <inputs>
-        <param name="input_bam" type="data" format="bam" label="BAM dataset to split by mapped/unmapped"/>
-    </inputs>
-    <outputs>
-        <data format="bam" name="mapped" label="${input_bam.name} mapped" from_work_dir="split_bam.MAPPED.bam" />
-        <data format="bam" name="unmapped" label="${input_bam.name} unmapped" from_work_dir="split_bam.UNMAPPED.bam" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
-            <output name="mapped" file="split_bam.MAPPED.bam"  compare="sim_size" delta="200" />
-            <output name="unmapped" file="split_bam.UNMAPPED.bam"  compare="sim_size" delta="200" />
-        </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
-
-
-**How it works**
-
-Splits the input BAM file into 2 output files named (MAPPED) and (UNMAPPED) containing mapped and unmapped reads, respectively.
-
------
-
-.. 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>
diff -r 9dbf707bebb0 -r 20ad2e231693 bamtools_split_paired.xml
--- a/bamtools_split_paired.xml	Wed Jan 11 12:03:53 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-<tool id="bamtools_split_paired" name="Split BAM by Paired/Single End" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description></description>
-    <macros>
-          <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <command>
-        <![CDATA[
-            ln -s '${input_bam}' 'localbam.bam' &&
-            ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' &&
-            bamtools split -paired
-            -in localbam.bam
-            -stub split_bam
-        ]]>
-    </command>
-    <inputs>
-        <param name="input_bam" type="data" format="bam" label="BAM dataset to split by single_end/paired_end"/>
-    </inputs>
-    <outputs>
-        <data format="bam" name="single" label="${input_bam.name} mapped" from_work_dir="split_bam.SINGLE_END.bam" />
-        <data format="bam" name="paired" label="${input_bam.name} unmapped" from_work_dir="split_bam.PAIRED_END.bam" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="input_bam" ftype="bam" value="bamtools-input-paired.bam"/>
-            <output name="single" file="split_bam.SINGLE_END.bam"  compare="sim_size" delta="200" />
-            <output name="paired" file="split_bam.PAIRED_END.bam"  compare="sim_size" delta="200" />
-        </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
-
-
-**How it works**
-
-
-Splits the input BAM file into 2 output files named (SINGLE_END) and (PAIRED_END) containing single_end and paired_end reads, respectively.
-
------
-
-.. 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>
diff -r 9dbf707bebb0 -r 20ad2e231693 bamtools_split_tag.xml
--- a/bamtools_split_tag.xml	Wed Jan 11 12:03:53 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-<tool id="bamtools_split_tag" name="Split BAM by Tag" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>into dataset list collection</description>
-    <macros>
-          <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <command>
-        <![CDATA[
-            #import re
-            #set $name = 'split_bam' + $re.sub('\W','_',$re.sub('\.bam$','',$input_bam.name))
-            ln -s '${input_bam}' 'localbam.bam' &&
-            ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' &&
-            bamtools split -tag $tag_name
-            -in 'localbam.bam'
-            -stub '$name'
-        ]]>
-    </command>
-    <inputs>
-        <param name="input_bam" type="data" format="bam" label="BAM dataset to split by tag value"/>
-        <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;"/>
-    </inputs>
-    <outputs>
-        <collection name="output_bams" type="list" label="${input_bam.name} Split List">
-            <discover_datasets pattern="split_bam(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="false"/>
-        </collection>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input_bam" ftype="bam" value="bamtools-input-tags.bam"/>
-            <param name="tag_name" value="XG"/>
-            <output_collection name="output_bams"  type="list">
-                <element name="bamtools_input_tags.TAG_XG_V"  file="bamtools_input_tags.TAG_XG_V.bam" 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 tag value can produce very large numbers of outputs. Read below and know what you are doing.
-
------
-
-**How it works**
-
-Split alignments by tag name into a dataset list collection.
-
-This can generate a huge number of output datasets depending on the number of distinct values of the TAG.
-
-
------
-
-.. 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>