# HG changeset patch
# User iuc
# Date 1632844695 0
# Node ID c701f5f96f32c6e271babaa02db65a7a875ee55e
# Parent  428d5c102c96c4a8a5131d91f7a1dac801eb0807
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"

diff -r 428d5c102c96 -r c701f5f96f32 macros.xml
--- a/macros.xml	Thu Oct 10 03:39:03 2019 -0400
+++ b/macros.xml	Tue Sep 28 15:58:15 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 428d5c102c96 -r c701f5f96f32 sam_to_bam.xml
--- a/sam_to_bam.xml	Thu Oct 10 03:39:03 2019 -0400
+++ b/sam_to_bam.xml	Tue Sep 28 15:58:15 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.1">
+<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.2" profile="@PROFILE@">
     <description>convert SAM to BAM</description>
 
     <macros>
@@ -9,62 +9,39 @@
     <expand macro="version_command"/>
 
     <command><![CDATA[
-        #if $source.index_source == "history":
-            ln -s '${source.ref_file}' input.fa &&
-            samtools faidx input.fa &&
-        #else
-            ln -s '${source.index.fields.path}' input.fa &&
-            ln -s '${source.index.fields.path}.fai' input.fa.fai &&
-        #end if
+        @ADDTHREADS@
+        @ADDMEMORY@
+        @PREPARE_FASTA_IDX@
 
         samtools view
             -b
-            -@ \${GALAXY_SLOTS:-1}
-            -t input.fa.fai '$input1' |
+            -@ \$addthreads
+            -t '$reffai'
+            '$input' |
 
         samtools sort
             -O bam
-            -@ \${GALAXY_SLOTS:-1}
+            -@ \$addthreads -m \$addmemory"M"
             -o '$output1'
             -T "\${TMPDIR:-.}"
     ]]></command>
 
     <inputs>
-        <conditional name="source">
-            <param label="Choose the source for the reference genome" name="index_source" type="select">
-                <option value="cached">Use a built-in genome</option>
-                <option value="history">Use a genome from the history</option>
-            </param>
-            <when value="cached">
-                <param name="input1" type="data" format="sam" label="SAM file to convert">
-                    <validator type="unspecified_build" />
-                    <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />
-                </param>
-                <param name="index" type="select" label="Using reference genome">
-                    <options from_data_table="fasta_indexes">
-                        <filter column="dbkey" key="dbkey" ref="input1" type="data_meta" />
-                        <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
-                    </options>
-                </param>
-            </when>
-            <when value="history">
-                <param name="input1" type="data" format="sam" label="SAM file to convert" />
-                <param name="ref_file" type="data" format="fasta" label="Using reference file" />
-            </when>
-        </conditional>
+        <param name="input" type="data" format="sam" label="SAM file to convert"/>
+        <expand macro="mandatory_reference" argument="-t"/>
     </inputs>
     <outputs>
         <data name="output1" format="bam" label="${tool.name} on ${on_string}: converted BAM">
             <actions>
-                <conditional name="source.index_source">
+                <conditional name="addref_cond.addref_select">
                     <when value="cached">
                         <action name="dbkey" type="metadata">
-                            <option name="source.input1" param_attribute="dbkey" type="from_param" />
+                            <option name="input" param_attribute="dbkey" type="from_param" />
                         </action>
                     </when>
                     <when value="history">
                         <action name="dbkey" type="metadata">
-                            <option name="source.ref_file" param_attribute="dbkey" type="from_param" />
+                            <option name="addref_cond.ref" param_attribute="dbkey" type="from_param" />
                         </action>
                     </when>
                 </conditional>
@@ -73,22 +50,22 @@
     </outputs>
     <tests>
         <test>
-            <param name="index_source" value="history" />
-            <param name="input1" ftype="sam" value="sam_to_bam_in1.sam" />
-            <param name="ref_file" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
-            <output name="output1" ftype="bam" file="sam_to_bam_out1.bam" />
+            <param name="addref_select" value="history" />
+            <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
+            <param name="input" ftype="sam" value="sam_to_bam_in1.sam" />
+            <output name="output1" ftype="bam" file="sam_to_bam_out1.bam" lines_diff="4"/>
         </test>
         <test>
-            <param name="index_source" value="cached" />
-            <param name="input1" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" />
-            <param name="index" value="equCab2chrM" />
-            <output name="output1" ftype="bam" file="sam_to_bam_out2.bam" />
+            <param name="addref_select" value="cached" />
+            <param name="ref" value="equCab2chrM" />
+            <param name="input" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" />
+            <output name="output1" ftype="bam" file="sam_to_bam_out2.bam" lines_diff="4"/>
         </test>
         <test>
-            <param name="index_source" value="history" />
-            <param name="input1" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
-            <param name="ref_file" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
-            <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" />
+            <param name="addref_select" value="history" />
+            <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
+            <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
+            <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r 428d5c102c96 -r c701f5f96f32 test-data/sam_to_bam_out1.bam
Binary file test-data/sam_to_bam_out1.bam has changed
diff -r 428d5c102c96 -r c701f5f96f32 test-data/sam_to_bam_out2.bam
Binary file test-data/sam_to_bam_out2.bam has changed
diff -r 428d5c102c96 -r c701f5f96f32 test-data/sam_to_bam_out3.bam
Binary file test-data/sam_to_bam_out3.bam has changed