# HG changeset patch
# User iuc
# Date 1632845118 0
# Node ID 2504000d5158377d7dcc82b13782ccc9f2b60eca
# Parent  dd8305e4e58ecc67249c353ebcf52c74fc7a0f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"

diff -r dd8305e4e58e -r 2504000d5158 macros.xml
--- a/macros.xml	Sun Jul 28 14:49:27 2019 -0400
+++ b/macros.xml	Tue Sep 28 16:05:18 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 dd8305e4e58e -r 2504000d5158 samtools_phase.xml
--- a/samtools_phase.xml	Sun Jul 28 14:49:27 2019 -0400
+++ b/samtools_phase.xml	Tue Sep 28 16:05:18 2021 +0000
@@ -1,5 +1,5 @@
-<tool id="samtools_phase" name="Call and phase" version="2.0.1">
-    <description>heterozygous SNPs</description>
+<tool id="samtools_phase" name="Samtools phase" version="2.0.2" profile="@PROFILE@">
+    <description>call and phase heterozygous SNPs</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -49,16 +49,16 @@
     </outputs>
     <tests>
         <test>
-            <param name="option_sets" value="default" /> 
-            <param name="input_bam" value="samtools_phase_in_1.bam" /> 
+            <param name="option_sets" value="default" />
+            <param name="input_bam" value="samtools_phase_in_1.bam" />
             <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" />
-            <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" />
-            <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" />
-            <output name="chimera" file="empty_file.bam" ftype="bam" />
+            <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" lines_diff="4" />
+            <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" lines_diff="4" />
+            <output name="chimera" file="empty_file_1.bam" ftype="bam" lines_diff="4" />
         </test>
         <test>
-            <param name="input_bam" value="samtools_phase_in_2.bam" /> 
-            <param name="option_sets" value="advanced" /> 
+            <param name="input_bam" value="samtools_phase_in_2.bam" />
+            <param name="option_sets" value="advanced" />
             <param name="option_set|block_length" value="13" />
             <param name="option_set|min_het" value="37" />
             <param name="option_set|min_bq" value="13" />
@@ -66,13 +66,13 @@
             <param name="option_set|ignore_chimeras" value="false" />
             <param name="option_set|drop_ambiguous" value="true" />
             <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" />
-            <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" />
-            <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" />
-            <output name="chimera" file="samtools_phase_out_2_chimera.bam" />
+            <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" lines_diff="4" />
+            <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" lines_diff="4" />
+            <output name="chimera" file="samtools_phase_out_2_chimera.bam" ftype="bam" lines_diff="4" />
         </test>
         <test>
-            <param name="input_bam" value="samtools_phase_in_2.bam" /> 
-            <param name="option_sets" value="advanced" /> 
+            <param name="input_bam" value="samtools_phase_in_2.bam" />
+            <param name="option_sets" value="advanced" />
             <param name="option_set|block_length" value="13" />
             <param name="option_set|min_het" value="37" />
             <param name="option_set|min_bq" value="13" />
@@ -80,9 +80,9 @@
             <param name="option_set|ignore_chimeras" value="true" />
             <param name="option_set|drop_ambiguous" value="false" />
             <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" />
-            <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" />
-            <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" />
-            <output name="chimera" file="empty_file.bam"/>
+            <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" lines_diff="4" />
+            <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" lines_diff="4" />
+            <output name="chimera" file="empty_file_3.bam" ftype="bam" lines_diff="4" />
         </test>
     </tests>
     <help><![CDATA[
diff -r dd8305e4e58e -r 2504000d5158 test-data/empty_file.bam
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diff -r dd8305e4e58e -r 2504000d5158 test-data/empty_file_1.bam
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diff -r dd8305e4e58e -r 2504000d5158 test-data/empty_file_3.bam
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diff -r dd8305e4e58e -r 2504000d5158 test-data/samtools_phase_out_1_phase0.bam
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diff -r dd8305e4e58e -r 2504000d5158 test-data/samtools_phase_out_1_phase1.bam
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diff -r dd8305e4e58e -r 2504000d5158 test-data/samtools_phase_out_2_chimera.bam
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diff -r dd8305e4e58e -r 2504000d5158 test-data/samtools_phase_out_2_phase0.bam
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diff -r dd8305e4e58e -r 2504000d5158 test-data/samtools_phase_out_2_phase1.bam
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diff -r dd8305e4e58e -r 2504000d5158 test-data/samtools_phase_out_3_phase0.bam
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diff -r dd8305e4e58e -r 2504000d5158 test-data/samtools_phase_out_3_phase1.bam
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