# HG changeset patch
# User iuc
# Date 1493281059 14400
# Node ID f42f9ae6d1092db662514aa74078b732126a82ed
# Parent  880c3cb5a5a6a73b297712d32c68808587d0024c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e

diff -r 880c3cb5a5a6 -r f42f9ae6d109 macros.xml
--- a/macros.xml	Fri Apr 07 11:47:36 2017 -0400
+++ b/macros.xml	Thu Apr 27 04:17:39 2017 -0400
@@ -2,14 +2,14 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.42">stacks</requirement>
+            <requirement type="package" version="1.46">stacks</requirement>
             <requirement type="package" version="1.2.10">velvet</requirement>
-            <container type="docker">quay.io/biocontainers/stacks:1.42--2</container>
+            <requirement type="package" version="1.1">stacks_summary</requirement>
             <yield/>
         </requirements>
     </xml>
 
-    <token name="@WRAPPER_VERSION@">1.42</token>
+    <token name="@WRAPPER_VERSION@">1.46</token>
 
     <xml name="stdio">
         <stdio>
@@ -90,6 +90,7 @@
         <option value="bsaHI">bsaHI</option>
         <option value="hpaII">hpaII</option>
         <option value="ncoI">ncoI</option>
+        <option value="ApaLI">ApaLI</option>
     </xml>
 
     <xml name="cross_types">
@@ -100,6 +101,19 @@
         <option value="GEN">GEN (generic, unspecific to any map type)</option>
     </xml>
 
+    <token name="@CLEAN_EXT@">
+        <![CDATA[
+        #from os.path import splitext
+        #import re
+        #def clean_ext($identifier)
+            #while $identifier.endswith(('.1', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam'))
+                #set $identifier = splitext($identifier)[0]
+            #end while
+$identifier#slurp
+        #end def
+        ]]>
+    </token>
+
     <token name="@NORM_GENOTYPES_OUTPUT_LIGHT@">
         <![CDATA[
         ## We need to do this as the output file names contains the value of an option (min progeny)
diff -r 880c3cb5a5a6 -r f42f9ae6d109 stacks_pstacks.xml
--- a/stacks_pstacks.xml	Fri Apr 07 11:47:36 2017 -0400
+++ b/stacks_pstacks.xml	Thu Apr 27 04:17:39 2017 -0400
@@ -6,26 +6,22 @@
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
-        #from os.path import splitext
-        #import re
+
+        @CLEAN_EXT@
 
         mkdir stacks_inputs stacks_outputs
 
         &&
 
-        #if $sample.is_of_type('sam'):
-            #set $data_path = splitext($sample.element_identifier)[0]
-            #set $data_path = re.sub(r'\.1$', '', $data_path)
-            #set $data_path = "stacks_inputs/" + $data_path + ".sam"
+        #if $sample.is_of_type('sam')
+            #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".sam"
             #set inputype = "sam"
-        #else:
-            #set $data_path = splitext($sample.element_identifier)[0]
-            #set $data_path = re.sub(r'\.1$', '', $data_path)
-            #set $data_path = "stacks_inputs/" + $data_path + ".bam"
+        #else
+            #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".bam"
             #set inputype = "bam"
         #end if
 
-        ln -s "${sample}" "${data_path}"
+        ln -s '${sample}' '${data_path}'
 
         &&
 
@@ -42,13 +38,17 @@
 
             -m $m
 
+            --max_clipped $max_clipped
+            --min_mapq $min_mapq
+            $keep_sec_alns
+
             ## snp_model
-            #if str( $snp_options.select_model.model_type) == "bounded":
+            #if str( $snp_options.select_model.model_type) == "bounded"
                 --model_type bounded
                 --bound_low $snp_options.select_model.bound_low
                 --bound_high $snp_options.select_model.bound_high
                 --alpha $snp_options.select_model.alpha
-            #else if str( $snp_options.select_model.model_type) == "snp":
+            #else if str( $snp_options.select_model.model_type) == "snp"
                 --model_type snp
                 --alpha $snp_options.select_model.alpha
             #else
@@ -58,19 +58,28 @@
 
             -o stacks_outputs
 
-             > pstacks.log 2>&1
+             2>&1 | tee pstacks.log
 
             ## If input is in bam format, stacks will output gzipped files (no option to control this)
             && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi
+
+            &&
+
+            stacks_summary.py --stacks-prog pstacks --res-dir stacks_outputs --logfile pstacks.log --summary stacks_outputs/summary.html
     ]]></command>
 
     <inputs>
-        <param name="sample" argument="-f" format="fastqsanger,fasta" type="data" label="Input short reads from an individual" />
+        <param name="sample" argument="-f" format="sam,bam" type="data" label="Input short reads from an individual" />
 
         <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/>
 
         <param name="m" argument="-m" type="integer" value="1" label="Minimum depth of coverage required to create a stack"/>
 
+        <param name="max_clipped" argument="--max_clipped" type="float" value="0.15" min="0.0" max="1.0" label="Alignments with more than this fraction of soft-clipped bases are discarded"/>
+
+        <param name="min_mapq" argument="--min_mapq" type="integer" value="10" label="Minimum required mapping quality"/>
+
+        <param name="keep_sec_alns" argument="--keep_sec_alns" type="boolean" checked="false" truevalue="--keep_sec_alns" falsevalue="" label="Keep secondary alignments" />
 
         <!-- SNP Model options -->
         <section name="snp_options" title="SNP Model Options (pstacks options)" expanded="False">
@@ -80,6 +89,9 @@
 
     <outputs>
         <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" />
+
+        <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
+
         <collection name="tabs" type="list" label="Stacks from ${on_string}">
             <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
             <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
@@ -98,6 +110,11 @@
                     <has_text text="done." />
                 </assert_contents>
             </output>
+            <output name="output_summary">
+                <assert_contents>
+                    <has_text text="Stacks Statistics" />
+                </assert_contents>
+            </output>
 
             <output_collection name="tabs">
                 <element name="PopA_01.tags">
diff -r 880c3cb5a5a6 -r f42f9ae6d109 test-data/demultiplexed/PopA_01.1.fq.gzip
Binary file test-data/demultiplexed/PopA_01.1.fq.gzip has changed
diff -r 880c3cb5a5a6 -r f42f9ae6d109 test-data/denovo_map/popmap_cstacks.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/denovo_map/popmap_cstacks.tsv	Thu Apr 27 04:17:39 2017 -0400
@@ -0,0 +1,1 @@
+PopA_01	myPopA
diff -r 880c3cb5a5a6 -r f42f9ae6d109 test-data/procrad/R1.fq.gzip
Binary file test-data/procrad/R1.fq.gzip has changed
diff -r 880c3cb5a5a6 -r f42f9ae6d109 test-data/ustacks/ustacks.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ustacks/ustacks.out	Thu Apr 27 04:17:39 2017 -0400
@@ -0,0 +1,41 @@
+ustacks parameters selected:
+  Sample ID: 1
+  Min depth of coverage to create a stack: 2
+  Max distance allowed between stacks: 2
+  Max distance allowed to align secondary reads: 4
+  Max number of stacks allowed per de novo locus: 3
+  Deleveraging algorithm: disabled
+  Removal algorithm: enabled
+  Model type: SNP
+  Alpha significance level for model: 0.05
+  Gapped alignments: disabled
+Parsing stacks_inputs/PopA_01.fq
+Loading RAD-Tags...done
+Loaded 66 RAD-Tags.
+  Inserted 7 elements into the RAD-Tags hash map.
+  0 reads contained uncalled nucleotides that were modified.
+4 initial stacks were populated; 3 stacks were set aside as secondary reads.
+Initial coverage mean: 15.75; Std Dev: 7.46241; Max: 27
+Deleveraging trigger: 23; Removal trigger: 31
+Calculating distance for removing repetitive stacks.
+  Distance allowed between stacks: 1; searching with a k-mer length of 47 (48 k-mers per read); 1 k-mer hits required.
+Removing repetitive stacks.
+  Removed 0 stacks.
+  4 stacks remain for merging.
+Post-Repeat Removal, coverage depth Mean: 15.75; Std Dev: 7.46241; Max: 27
+Calculating distance between stacks...
+  Distance allowed between stacks: 2; searching with a k-mer length of 31 (64 k-mers per read); 2 k-mer hits required.
+Merging stacks, maximum allowed distance: 2 nucleotide(s)
+  4 stacks merged into 3 loci; deleveraged 0 loci; blacklisted 0 loci.
+After merging, coverage depth Mean: 21; Std Dev: 4.24264; Max: 27
+Merging remainder radtags
+  3 remainder sequences left to merge.
+  Distance allowed between stacks: 4; searching with a k-mer length of 17 (78 k-mers per read); 10 k-mer hits required.
+  Matched 3 remainder reads; unable to match 0 remainder reads.
+After remainders merged, coverage depth Mean: 22; Std Dev: 4.32049; Max: 28
+Calling final consensus sequences, invoking SNP-calling model...
+Number of utilized reads: 66
+Writing loci, SNPs, and alleles to 'stacks_outputs/'...
+  Refetching sequencing IDs from stacks_inputs/PopA_01.fq... read 66 sequence IDs.
+done.
+ustacks is done.