Repository 'stacks2_gstacks'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks

Changeset 1:27359c6bf3e3 (2019-09-30)
Previous changeset 0:d35cb34f2b85 (2019-07-01) Next changeset 2:1d839ead7ad3 (2020-07-15)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
modified:
macros.xml
macros_process.xml
stacks_gstacks.xml
added:
test-data/procrad/process_radtags2.out
b
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
b
@@ -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." />
b
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
b
@@ -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"/>
b
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
b
@@ -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>
b
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
b
@@ -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