# HG changeset patch
# User iuc
# Date 1569867557 14400
# Node ID 27359c6bf3e30d5ab9afe1cfd4154653ac39dfa8
# Parent  d35cb34f2b850f0480eb2f0616c71aba53f0641c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"

diff -r d35cb34f2b85 -r 27359c6bf3e3 macros.xml
--- a/macros.xml	Mon Jul 01 10:59:14 2019 -0400
+++ b/macros.xml	Mon Sep 30 14:19:17 2019 -0400
@@ -8,7 +8,7 @@
     </xml>
 
     <token name="@STACKS_VERSION@">2.4</token>
-    <token name="@WRAPPER_VERSION@">0</token>
+    <token name="@WRAPPER_VERSION@">1</token>
     <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 -->
     <token name="@PROFILE@">18.01</token>
 
@@ -216,8 +216,8 @@
         </expand>
     </xml>
 
-    <!-- fastq input (used in denovomap, tsv2bam, ustacks) 
-         - fastq_optional: makes fastq input optional (true/false) 
+    <!-- fastq input (used in denovomap, tsv2bam, ustacks)
+         - fastq_optional: makes fastq input optional (true/false)
          - se_option: wording for "single end" option (for tsv2bam this is the
               reverse reads for the others its the forward reads)
          - help: help text -->
@@ -568,10 +568,10 @@
         </expand>
     </xml>
 
-	<!-- variant calling option for use in gstacks and denovomap 
+	<!-- variant calling option for use in gstacks and denovomap
          default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap)
          otherwise no default is is available and gstacks will output and error
-         "Error: No value was provided for \-\-var-alpha and there is no default for this model)" 
+         "Error: No value was provided for \-\-var-alpha and there is no default for this model)"
 	-->
     <xml name="variant_calling_options_vg" token_varalpha_default="">
         <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available." />
diff -r d35cb34f2b85 -r 27359c6bf3e3 macros_process.xml
--- a/macros_process.xml	Mon Jul 01 10:59:14 2019 -0400
+++ b/macros_process.xml	Mon Sep 30 14:19:17 2019 -0400
@@ -75,7 +75,7 @@
                 <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded" />
                 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" />
                 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
-                <param argument="--filter_illumina" type="boolean" checked="false" truevalue="--filter_illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing" />
+                <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing" />
             </when>
             <when value="no">
                 <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="useful if your data has already been trimmed"/>
diff -r d35cb34f2b85 -r 27359c6bf3e3 stacks_gstacks.xml
--- a/stacks_gstacks.xml	Mon Jul 01 10:59:14 2019 -0400
+++ b/stacks_gstacks.xml	Mon Sep 30 14:19:17 2019 -0400
@@ -11,6 +11,14 @@
 @FASTQ_INPUT_FUNCTIONS@
 
 mkdir bam_inputs stacks_outputs &&
+
+## annoyingly gstacks creates stacks_output/gstacks.log
+## instead of just writing to stderr as the other tools
+## hence we do not use the tokens and return populations.log as log file and take the stderr
+#if $output_log
+    ln -s '$output_log' stacks_outputs/gstacks.log &&
+#end if
+
 #if $mode_cond.mode_select == "denovo" and not $popmap:
     ## since collections have no len .. yet
     #try:
@@ -88,14 +96,6 @@
     #end if
 #end if
 
-
-## annoyingly gstacks creates stacks_output/gstacks.log
-## instead of just writing to stderr as the other tools
-## hence we do not use the tokens and return populations.log as log file and take the stderr
-#if $output_log
-    && mv stacks_outputs/gstacks.log $output_log
-#end if
-
 @EXTRACT_VCF@
 
 ## TODO extract individual distributions from stacks_outputs/gstacks.log.distribs
@@ -250,7 +250,6 @@
             <param name="add_log" value="yes" />
             <assert_command>
                 <has_text text="--ignore-pe-reads" />
-                <has_text text="--rm-pcr-duplicates" />
                 <has_text text="--kmer-length 23" />
                 <has_text text="--max-debruijn-reads 666" />
                 <has_text text="--min-kmer-cov 3" />
@@ -270,15 +269,15 @@
                 <param name="mode_select" value="refbased"/>
                 <conditional name="paired_cond">
                     <param name="paired_select" value=""/>
-                    <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes to much of the test data and gstacks fails-->
+                    <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes too much of the test data and gstacks fails-->
                     <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates" />
                 </conditional>
             </conditional>
             <param name="add_log" value="yes" />
             <assert_command>
-                <has_text text="-I bam_inputs" />
-                <not_has_text text="-B " />
-                <has_text text="--rm-unpaired-reads" />
+                <not_has_text text="-I bam_inputs" />
+                <has_text text="-B " />
+                <not_has_text text="--rm-unpaired-reads" />
                 <has_text text="--rm-pcr-duplicates" />
             </assert_command>
         </test>
@@ -296,7 +295,7 @@
                     <param name="min_mapq" value="23" />
                     <param name="max_clipped" value="0.23" />
                     <param name="max_insert_len" value="666" />
-                    <param name="details" value="--detailed"/>
+                    <param name="details" value="--details"/>
                     <param name="phasing_cooccurrences_thr_min" value="2"/>
                     <param name="phasing_cooccurrences_thr_max" value="3"/>
                     <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" />
@@ -307,13 +306,13 @@
             <param name="model_cond|var_alpha" value="0.1" />
             <param name="add_log" value="yes" />
             <assert_command>
-                <not_has_text text="-I bam_inputs" />
-                <has_text text="-B " />
+                <has_text text="-I bam_inputs" />
+                <not_has_text text="-B " />
                 <has_text text="--unpaired" />
                 <has_text text="--min-mapq 23" />
                 <has_text text="--max-clipped 0.23" />
                 <has_text text="--max-insert-len 666" />
-                <has_text text="--detailed" />
+                <has_text text="--details" />
                 <has_text text="--phasing-cooccurrences-thr-range 2,3" />
                 <has_text text="--phasing-dont-prune-hets" />
                 <has_text text="--model snp" />
@@ -333,8 +332,8 @@
             </conditional>
             <param name="add_log" value="yes" />
             <assert_command>
-                <has_text text="-I bam_inputs" />
-                <not_has_text text="-B " />
+                <not_has_text text="-I bam_inputs" />
+                <has_text text="-B " />
                 <has_text text="--ignore-pe-reads" />
             </assert_command>
             <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
diff -r d35cb34f2b85 -r 27359c6bf3e3 test-data/procrad/process_radtags2.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/procrad/process_radtags2.out	Mon Sep 30 14:19:17 2019 -0400
@@ -0,0 +1,88 @@
+process_radtags v2.4, executed 2019-09-30 14:57:00 (zlib-1.2.11)
+process_radtags -p stacks_inputs/ -i gzfastq -b /tmp/tmpe_shit/files/d/e/d/dataset_ded45538-15ef-471f-9585-07ee09b6e6d4.dat --inline_null -y gzfastq -o stacks_outputs -w 0.1 -s 11 -c -q -D -e ecoRI
+File	Retained Reads	Low Quality	Barcode Not Found	RAD cutsite Not Found	Total
+R1.fastq.gz	2222	0	0	4778	7000
+R2.fastq.gz	0	0	7000	0	7000
+
+Total Sequences	14000
+Barcode Not Found	7000
+Low Quality	0
+RAD Cutsite Not Found	4778
+Retained Reads	2222
+
+Barcode	Filename	Total	NoRadTag	LowQuality	Retained
+ATGGGG	PopA_01	160	94	0	66
+GGGTAA	PopA_02	146	86	0	60
+AGGAAA	PopA_03	224	132	0	92
+TTTAAG	PopA_04	168	146	0	22
+GGTGTG	PopA_05	220	154	0	66
+TGATGT	PopA_06	214	147	0	67
+GGTTGT	PopA_07	182	137	0	45
+ATAAGT	PopA_08	232	164	0	68
+AAGATA	PopA_09	182	134	0	48
+TGTGAG	PopA_10	168	128	0	40
+ATAGTT	PopA_11	200	132	0	68
+GGAAGG	PopA_12	178	136	0	42
+TTTGTG	PopA_13	190	152	0	38
+TTAAAT	PopA_14	166	96	0	70
+AATAAG	PopA_15	152	74	0	78
+AAGAGG	PopA_16	174	112	0	62
+TAGTGT	PopA_17	242	146	0	96
+TGGAAG	PopA_18	148	98	0	50
+GGGTTG	PopA_19	110	64	0	46
+CATCAT	PopA_20	178	144	0	34
+GGAGAG	PopB_20	210	142	0	68
+GTTTTA	PopB_01	136	90	0	46
+TGATAA	PopB_02	166	108	0	58
+GTTGAT	PopB_03	148	74	0	74
+AGATTA	PopB_04	180	156	0	24
+GTATAG	PopB_05	136	106	0	30
+TTGGGA	PopB_06	166	112	0	54
+ATATAT	PopB_07	242	156	0	86
+GATGAG	PopB_08	208	152	0	56
+GGGAAT	PopB_09	198	126	0	72
+AGTAAT	PopB_10	164	120	0	44
+GGGATA	PopB_11	146	90	0	56
+GAGAAG	PopB_12	162	110	0	52
+AGTAGA	PopB_13	204	146	0	58
+AAGGAT	PopB_14	180	128	0	52
+AGGGTA	PopB_15	134	72	0	62
+TGTTTT	PopB_16	138	98	0	40
+ATGATG	PopB_17	142	100	0	42
+GAGTTA	PopB_18	160	112	0	48
+ATGTAG	PopB_19	146	104	0	42
+
+Sequences not recorded
+Barcode	Total
+CCGGTG	772
+CCGCGC	750
+CCGACA	743
+CCGGTC	723
+CCGCCT	695
+CCGTGG	675
+CCGGTT	667
+CCGATC	579
+CCGTGT	417
+CCGTAT	252
+CCGCGT	198
+CCGCGG	150
+CCGCAT	117
+CCGTTC	94
+CCGTAC	38
+CCGGGA	32
+CCGGAG	26
+CCGAAC	24
+CCGAGT	18
+CCGTGA	10
+CCGGGT	7
+CCGCTT	2
+CCGACG	2
+CCGATT	1
+CCGCCC	1
+CCGGCA	1
+CCGGCT	1
+CCGGGG	1
+CCGCCG	1
+CCGTGC	1
+CCGTAG	1
+CCGACT	1