# HG changeset patch
# User iuc
# Date 1632845185 0
# Node ID 88d7ed7fd423edda0aa42fb01d59a6fbd5743977
# Parent  bfeeedad5354919265d0fb7148f5274b0f98283d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"

diff -r bfeeedad5354 -r 88d7ed7fd423 macros.xml
--- a/macros.xml	Thu Sep 05 19:33:00 2019 -0400
+++ b/macros.xml	Tue Sep 28 16:06:25 2021 +0000
@@ -5,10 +5,16 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">1.9</token>
-    <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
+    <token name="@TOOL_VERSION@">1.13</token>
+    <token name="@PROFILE@">20.05</token>
+    <token name="@FLAGS@"><![CDATA[
+        #set $flags = 0
+        #if $filter
+            #set $flags = sum(map(int, str($filter).split(',')))
+        #end if
+    ]]></token>
     <token name="@PREPARE_IDX@"><![CDATA[
-        ##prepare input and indices 
+        ##prepare input and indices
         ln -s '$input' infile &&
         #if $input.is_of_type('bam'):
             #if str( $input.metadata.bam_index ) != "None":
@@ -25,7 +31,7 @@
         #end if
     ]]></token>
     <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
-        ##prepare input and indices 
+        ##prepare input and indices
         #for $i, $bam in enumerate( $input_bams ):
             ln -s '$bam' '${i}' &&
             #if $bam.is_of_type('bam'):
@@ -63,6 +69,51 @@
             #set reffai=None
         #end if
     ]]></token>
+
+    <xml name="optional_reference">
+        <conditional name="addref_cond">
+            <param name="addref_select" type="select" label="Use a reference sequence">
+                <help>@HELP@</help>
+                <option value="no">No</option>
+                <option value="history">Use a genome/index from the history</option>
+                <option value="cached">Use a built-in genome</option>
+            </param>
+            <when value="no"/>
+            <when value="history">
+                <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
+            </when>
+            <when value="cached">
+                <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
+                    </options>
+                    <validator  type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="mandatory_reference" token_help="" token_argument="">
+        <conditional name="addref_cond">
+            <param name="addref_select" type="select" label="Use a reference sequence">
+                <help>@HELP@</help>
+                <option value="history">Use a genome/index from the history</option>
+                <option value="cached">Use a built-in genome</option>
+            </param>
+            <when value="history">
+                <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
+            </when>
+            <when value="cached">
+                <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
+                        <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
+                    </options>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+
+
     <token name="@ADDTHREADS@"><![CDATA[
         ##compute the number of ADDITIONAL threads to be used by samtools (-@)
         addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
@@ -70,28 +121,28 @@
     <token name="@ADDMEMORY@"><![CDATA[
         ##compute the number of memory available to samtools sort (-m)
         ##use only 75% of available: https://github.com/samtools/samtools/issues/831
-        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && 
+        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
         ((addmemory=addmemory*75/100)) &&
     ]]></token>
     <xml name="seed_input">
-       <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> 
+       <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
     </xml>
-    <xml name="flag_options">
-        <option value="1">read is paired</option>
-        <option value="2">read is mapped in a proper pair</option>
-        <option value="4">read is unmapped</option>
-        <option value="8">mate is unmapped</option>
-        <option value="16">read reverse strand</option>
-        <option value="32">mate reverse strand</option>
-        <option value="64">read is the first in a pair</option>
-        <option value="128">read is the second in a pair</option>
-        <option value="256">alignment or read is not primary</option>
-        <option value="512">read fails platform/vendor quality checks</option>
-        <option value="1024">read is a PCR or optical duplicate</option>
-        <option value="2048">supplementary alignment</option>
+    <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false">
+        <option value="1" selected="@S1@">Read is paired</option>
+        <option value="2" selected="@S2@">Read is mapped in a proper pair</option>
+        <option value="4" selected="@S4@">Read is unmapped</option>
+        <option value="8" selected="@S8@">Mate is unmapped</option>
+        <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option>
+        <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option>
+        <option value="64" selected="@S64@">Read is the first in a pair</option>
+        <option value="128" selected="@S128@">Read is the second in a pair</option>
+        <option value="256" selected="@S256@">Alignment of the read is not primary</option>
+        <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option>
+        <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option>
+        <option value="2048" selected="@S2048@">Alignment is supplementary</option>
     </xml>
 
-    <!-- region specification macros and tokens for tools that allow the specification 
+    <!-- region specification macros and tokens for tools that allow the specification
          of region by bed file / space separated list of regions -->
     <token name="@REGIONS_FILE@"><![CDATA[
         #if $cond_region.select_region == 'tab':
diff -r bfeeedad5354 -r 88d7ed7fd423 samtools_slice_bam.xml
--- a/samtools_slice_bam.xml	Thu Sep 05 19:33:00 2019 -0400
+++ b/samtools_slice_bam.xml	Tue Sep 28 16:06:25 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_slice_bam" name="Slice" version="2.0.1">
+<tool id="samtools_slice_bam" name="Slice" version="2.0.2" profile="@PROFILE@">
     <description>BAM by genomic regions</description>
     <macros>
         <import>macros.xml</import>
@@ -13,12 +13,12 @@
     ln -s '${input_bam.metadata.bam_index}' temp_input.bam.bai &&
 
     #if str($slice_method.slice_method_selector) == "bed":
-        samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam && 
+        samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam &&
     #elif str($slice_method.slice_method_selector) == "chr":
-        samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam 
+        samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
         ${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } &&
     #elif str($slice_method.slice_method_selector) == "man":
-        samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam 
+        samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
 
         #for $region in $slice_method.regions:
             "${region.chrom}:${region.start}-${region.end}"
@@ -83,13 +83,13 @@
             <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
             <param name="slice_method_selector" value="bed"/>
             <param name="input_interval" ftype="bed" value="bam-slice.bed" />
-            <output name="output_bam" file="bam-slice-test1.bam" ftype="bam" />
+            <output name="output_bam" file="bam-slice-test1.bam" ftype="bam" lines_diff="4" />
         </test>
         <test>
             <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
             <param name="slice_method_selector" value="chr"/>
             <param name="refs" value="chrM" />
-            <output name="output_bam" file="bam-slice-test2.bam" ftype="bam" />
+            <output name="output_bam" file="bam-slice-test2.bam" ftype="bam" lines_diff="4" />
         </test>
         <test>
             <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
@@ -97,7 +97,7 @@
             <param name="chrom" value="chrM" />
             <param name="start" value="1" />
             <param name="end" value="1000" />
-            <output name="output_bam" file="bam-slice-test3.bam" ftype="bam" />
+            <output name="output_bam" file="bam-slice-test3.bam" ftype="bam" lines_diff="4"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -106,7 +106,7 @@
 Allows to restrict (slice) input BAM dataset to a list of intervals defined in a BED file, individual chromosomes, or manually set list of coordinates.
 BED datasets can be obtained from **Get Data -> UCSC Main**.
 
-This tool is based on ``samtools view`` command. 
+This tool is based on ``samtools view`` command.
 
 @no-chrom-options@
     ]]></help>
diff -r bfeeedad5354 -r 88d7ed7fd423 test-data/bam-slice-test1.bam
Binary file test-data/bam-slice-test1.bam has changed
diff -r bfeeedad5354 -r 88d7ed7fd423 test-data/bam-slice-test2.bam
Binary file test-data/bam-slice-test2.bam has changed
diff -r bfeeedad5354 -r 88d7ed7fd423 test-data/bam-slice-test3.bam
Binary file test-data/bam-slice-test3.bam has changed