# HG changeset patch
# User iuc
# Date 1493281150 14400
# Node ID 8dc6a3afbe83b204f45b8fe1c3e8cfe03fcf2260
# Parent  639f2db87df06a15017dcf548ef0b4c5d46c9d05
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e

diff -r 639f2db87df0 -r 8dc6a3afbe83 macros.xml
--- a/macros.xml	Fri Apr 07 11:48:36 2017 -0400
+++ b/macros.xml	Thu Apr 27 04:19:10 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 639f2db87df0 -r 8dc6a3afbe83 stacks_genotypes.xml
--- a/stacks_genotypes.xml	Fri Apr 07 11:48:36 2017 -0400
+++ b/stacks_genotypes.xml	Thu Apr 27 04:19:10 2017 -0400
@@ -12,13 +12,13 @@
 
         &&
 
-        #for $input_file in $input_col:
+        #for $input_file in $input_col
             #set $filename = str($input_file.element_identifier)
-            #if not $filename.endswith('.tsv'):
+            #if not $filename.endswith('.tsv')
                 #set $filename = $filename + ".tsv"
             #end if
-            #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename):
-                ln -s "${input_file}" "stacks_outputs/${filename}" &&
+            #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename)
+                ln -s '${input_file}' 'stacks_outputs/${filename}' &&
             #end if
         #end for
 
@@ -30,34 +30,34 @@
             -t $options_usage.cross_type
             -o $options_usage.map_out.map_out_type
 
-            #if str( $options_usage.map_out.map_out_type ) == "genomic":
+            #if str( $options_usage.map_out.map_out_type ) == "genomic"
                 -e ${options_usage.map_out.enzyme}
             #end if
 
-            #if str($advanced_options.minprogeny):
+            #if str($advanced_options.minprogeny)
                 -r $advanced_options.minprogeny
             #end if
 
-            #if str($advanced_options.mindepth):
+            #if str($advanced_options.mindepth)
                 -m $advanced_options.mindepth
             #end if
 
-            #if str($advanced_options.lnl):
+            #if str($advanced_options.lnl)
                 --lnl_lim $advanced_options.lnl
             #end if
 
-            #if $advanced_options.blacklist:
-                -B "$advanced_options.blacklist"
+            #if $advanced_options.blacklist
+                -B '$advanced_options.blacklist'
             #end if
-            #if $advanced_options.whitelist:
-                -W "$advanced_options.whitelist"
+            #if $advanced_options.whitelist
+                -W '$advanced_options.whitelist'
             #end if
 
-            #if $advanced_options.manual_cor:
-                --corr_path "$advanced_options.manual_cor"
+            #if $advanced_options.manual_cor
+                --corr_path '$advanced_options.manual_cor'
             #end if
 
-            #if $options_autocorr.corrections:
+            #if $options_autocorr.corrections
                 -c
                 --min_hom_seqs $options_autocorr.hom
                 --min_het_seqs $options_autocorr.het
@@ -68,6 +68,10 @@
             -s
 
             @NORM_GENOTYPES_OUTPUT_FULL@
+
+            &&
+
+            stacks_summary.py --stacks-prog genotypes --res-dir stacks_outputs --summary stacks_outputs/summary.html
     ]]></command>
     <inputs>
         <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" />
@@ -85,6 +89,9 @@
                     <option value="rqtl">R/QTL</option>
                     <option value="genomic">Genomic</option>
                 </param>
+                <when value="joinmap"/>
+                <when value="onemap"/>
+                <when value="rqtl"/>
                 <when value="genomic">
                     <param name="enzyme" argument="-e" type="select" label="Restriction enzyme used" help="Only needed for Genomic output format">
                         <expand macro="enzymes"/>
@@ -120,6 +127,8 @@
     </inputs>
     <outputs>
         <expand macro="genotypes_output_full"/>
+
+        <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
     </outputs>
 
     <tests>
@@ -143,6 +152,12 @@
             <param name="cross_type" value="CP" />
             <param name="advanced_options|minprogeny" value="1" />
 
+            <output name="output_summary">
+                <assert_contents>
+                    <has_text text="Stacks Statistics" />
+                </assert_contents>
+            </output>
+
             <!-- genotypes -->
             <output name="out_generic_haplo">
                 <assert_contents>
diff -r 639f2db87df0 -r 8dc6a3afbe83 test-data/demultiplexed/PopA_01.1.fq.gzip
Binary file test-data/demultiplexed/PopA_01.1.fq.gzip has changed
diff -r 639f2db87df0 -r 8dc6a3afbe83 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 04:19:10 2017 -0400
@@ -0,0 +1,1 @@
+PopA_01	myPopA
diff -r 639f2db87df0 -r 8dc6a3afbe83 test-data/procrad/R1.fq.gzip
Binary file test-data/procrad/R1.fq.gzip has changed
diff -r 639f2db87df0 -r 8dc6a3afbe83 test-data/ustacks/ustacks.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ustacks/ustacks.out	Thu Apr 27 04:19:10 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.