# HG changeset patch
# User iuc
# Date 1543617975 18000
# Node ID e65c2cd0964c2e08006f5f5d409a7d956ffb50df
# Parent  33208952b99db463c790acaa11ad28c913d23ecf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c

diff -r 33208952b99d -r e65c2cd0964c macros.xml
--- a/macros.xml	Tue May 09 11:18:11 2017 -0400
+++ b/macros.xml	Fri Nov 30 17:46:15 2018 -0500
@@ -1,11 +1,131 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.3.1">samtools</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">1.3.1</token>
+    <token name="@TOOL_VERSION@">1.9</token>
+    <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
+    <token name="@PREPARE_IDX@"><![CDATA[
+        ##prepare input and indices 
+        ln -s '$input' infile &&
+        #if $input.is_of_type('bam'):
+            #if str( $input.metadata.bam_index ) != "None":
+                ln -s '${input.metadata.bam_index}' infile.bai &&
+            #else:
+                samtools index infile infile.bai &&
+            #end if
+        #elif $input.is_of_type('cram'):
+            #if str( $input.metadata.cram_index ) != "None":
+                ln -s '${input.metadata.cram_index}' infile.crai &&
+            #else:
+                samtools index infile infile.crai &&
+            #end if
+        #end if
+    ]]></token>
+    <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
+        ##prepare input and indices 
+        #for $i, $bam in enumerate( $input_bams ):
+            ln -s '$bam' '${i}' &&
+            #if $bam.is_of_type('bam'):
+                #if str( $bam.metadata.bam_index ) != "None":
+                    ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
+                #else:
+                    samtools index '${i}' '${i}.bai' &&
+                #end if
+            #elif $bam.is_of_type('cram'):
+                #if str( $bam.metadata.cram_index ) != "None":
+                    ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
+                #else:
+                    samtools index '${i}' '${i}.crai' &&
+                #end if
+            #end if
+        #end for
+    ]]></token>
+    <token name="@PREPARE_FASTA_IDX@"><![CDATA[
+        ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")
+        ##and sets the -t/-T parameters accordingly:
+        ##- in case of history a symbolic link is used because samtools (view) will generate
+        ##  the index which might not be possible in the directory containing the fasta file
+        ##- in case of cached the absolute path is used which allows to read the cram file
+        ##  without specifying the reference
+        #if $addref_cond.addref_select == "history":
+            ln -s '${addref_cond.ref}' reference.fa &&
+            samtools faidx reference.fa &&
+            #set reffa="reference.fa"
+            #set reffai="reference.fa.fai"
+        #elif $addref_cond.addref_select == "cached":
+            #set reffa=str($addref_cond.ref.fields.path)
+            #set reffai=str($addref_cond.ref.fields.path)+".fai"
+        #else
+            #set reffa=None
+            #set reffai=None
+        #end if
+    ]]></token>
+    <token name="@ADDTHREADS@"><![CDATA[
+        ##compute the number of ADDITIONAL threads to be used by samtools (-@)
+        addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
+    ]]></token>
+    <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=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." /> 
+    </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>
+
+    <!-- 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 $cond_region.select_region == 'tab':
+            -t '$cond_region.targetregions'
+        #end if
+    ]]></token>
+    <token name="@REGIONS_MANUAL@"><![CDATA[
+        #if $cond_region.select_region == 'text':
+            #for $i, $x in enumerate($cond_region.regions_repeat):
+               '${x.region}'
+            #end for
+        #end if
+    ]]></token>
+    <xml name="regions_macro">
+        <conditional name="cond_region">
+            <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
+                <option value="no" selected="True">No</option>
+                <option value="text">Manualy specify regions</option>
+                <option value="tab">Regions from tabular file</option>
+            </param>
+            <when value="no"/>
+            <when value="text">
+                <repeat name="regions_repeat" min="1" default="1" title="Regions">
+                    <param name="region" type="text" label="region" help="format chr:from-to">
+                        <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
+                    </param>
+                </repeat>
+            </when>
+            <when value="tab">
+                <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" />
+            </when>
+        </conditional>
+    </xml>
+
     <xml name="citations">
         <citations>
             <citation type="bibtex">
@@ -49,21 +169,4 @@
             <exit_code range="1:" level="fatal" description="Error" />
         </stdio>
     </xml>
-    <token name="@no-chrom-options@">
------
-
-.. class:: warningmark
-
-**No options available? How to re-detect metadata**
-
-If you see a &quot;No options available&quot; within the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
-
-1. Click on the **pencil** icon adjacent to the dataset in the history
-2. A new menu will appear in the center pane of the interface
-3. Click **Datatype** tab
-4. Set **New Type** to **BAM**
-5. Click **Save**
-
-The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
-    </token>
 </macros>
diff -r 33208952b99d -r e65c2cd0964c samtools_calmd.xml
--- a/samtools_calmd.xml	Tue May 09 11:18:11 2017 -0400
+++ b/samtools_calmd.xml	Fri Nov 30 17:46:15 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="samtools_calmd" name="CalMD" version="2.0.1">
+<tool id="samtools_calmd" name="CalMD" version="2.0.2">
     <description>recalculate MD/NM tags</description>
     <macros>
         <import>macros.xml</import>
@@ -16,8 +16,9 @@
         #end if
 
         samtools calmd
+            $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq
             #if str($option_set.option_sets) == 'advanced':
-                $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq
+                $option_set.change_identical -C $option_set.adjust_mq
             #end if
             -b
             '$input_bam'
@@ -43,17 +44,36 @@
                 <param name="ref_fasta" type="data" format="fasta" label="Using reference file" />
             </when>
         </conditional>
+        <conditional name="baq_settings">
+            <param name="use_baq" argument="-r" type="select"
+            label="Do you also want BAQ (Base Alignment Quality) scores to be calculated?">
+                <option value="">No</option>
+                <option value="-r">Yes, run BAQ calculation</option>
+            </param>
+            <when value="">
+                <param name="modify_quality" type="hidden" value="" />
+                <param name="extended_baq" type="hidden" value="" />
+            </when>
+            <when value="-r">
+                <param name="modify_quality" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false"
+                label="Use BAQ to cap read base qualities"
+                help="By default, BAQ scores are stored in a separate BQ tag, and the read base quality string is left untouched. When you enable this option, the BAQ scores will be used directly to modify the quality string instead." />
+                <param name="extended_baq" argument="-E" type="boolean" truevalue="-E" falsevalue="" checked="false" label="Extended BAQ for better sensitivity" />
+            </when>
+        </conditional>
         <conditional name="option_set">
-            <param name="option_sets" type="select" label="Options">
+            <param name="option_sets" type="select" label="Additional options">
                 <option value="default">Use defaults</option>
                 <option value="advanced">Advanced options</option>
             </param>
             <when value="default" />
             <when value="advanced">
-                <param name="change_identical" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" />
-                <param name="modify_quality" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" />
-                <param name="compute_cap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" />
-                <param name="extended_baq" argument="-E" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" />
+                <param name="change_identical" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False"
+                label="Change identical bases to '='"
+                help="Replace bases in read sequences that match the reference base at that position with an equal sign" />
+                <param name="adjust_mq" argument="-C" type="integer" min="0" max="255" value="0"
+                label="Coefficient to cap mapping quality of poorly mapped reads"
+                help="Higher values for this setting mean a stronger downgrade of the mapping quality of reads with excessive mismatches (50: recommended setting for reads aligned with BWA, 0: do not downgrade mapping qualities)" />
             </when>
         </conditional>
     </inputs>
@@ -62,6 +82,7 @@
     </outputs>
     <tests>
         <test>
+            <param name="use_baq" value="" />
             <param name="option_sets" value="default" />
             <param name="input_bam" value="phiX.bam"/>
             <param name="reference_source_selector" value="history" />
@@ -69,9 +90,11 @@
             <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
         </test>
         <test>
+            <param name="use_baq" value="-r" />
+            <param name="extended_baq" value="true" />
             <param name="option_sets" value="advanced" />
             <param name="change_identical" value="true" />
-            <param name="extended_baq" value="true" />
+            <param name="adjust_mq" value="50" />
             <param name="input_bam" value="phiX.bam"/>
             <param name="reference_source_selector" value="history" />
             <param name="ref_fasta" value="phiX.fasta" />
@@ -81,16 +104,27 @@
     <help><![CDATA[
 **What it does**
 
-Generates the MD tag using the ``samtools calmd`` command. If the MD tag (see SAM format reference below for explanation of SAM/BAM tags) is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file.
+Generates the MD tag using the ``samtools calmd`` command. If the MD tag (see
+SAM format reference below for explanation of SAM/BAM tags) is already present,
+this command will give a warning if the MD tag generated is different from the
+existing tag.
+
+Optionally, also generates the BQ tag to encode base alignment qualities,
+caps the mapping quality of poorly mapping reads, and modifies read sequences
+replacing bases matching the reference with ``=``.
+
+Outputs a BAM file.
 
 -----
 
-**NM and MD tags**
+**SAM/BAM tags written by this tool**
 
-From the SAM format specification::
+From the SAM format tag specification::
 
   MD (string)  String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7
-  NM (indeger) Edit distance to the reference, including ambiguous bases but excluding clipping
+  NM (integer) Edit distance to the reference, including ambiguous bases but excluding clipping
+  BQ (string)  String of offsets to base alignment quality (BAQ), of the same length as the read sequence. 
+               At the i-th read base, BAQ i = Q i − (BQ i − 64) where Q i is the i-th base quality.
 
 See references for more information about SAM format tags.
     ]]></help>
diff -r 33208952b99d -r e65c2cd0964c test-data/samtools_calmd_out_2.bam
Binary file test-data/samtools_calmd_out_2.bam has changed