# HG changeset patch
# User matthias
# Date 1561474771 14400
# Node ID dddd1a6454ce030d7c9ff187ab28bbac60d03d51
# Parent  3680074758c50ddec38ce5f910c476db8291d2e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 82e7263f3e57a29362d981e36b82b82063f12ac3

diff -r 3680074758c5 -r dddd1a6454ce macros.xml
--- a/macros.xml	Thu Jun 20 08:14:41 2019 -0400
+++ b/macros.xml	Tue Jun 25 10:59:31 2019 -0400
@@ -107,12 +107,12 @@
     <!-- log file handling -->
     <token name="@TEE_APPEND_LOG@"><![CDATA[
         #if $output_log
-            2>> $output_log &&
+            2>> '$output_log' &&
         #end if
     ]]></token>
     <token name="@CAT_LOG_TO_STDERR@"><![CDATA[
         #if $output_log
-            cat $output_log 2>&1
+            cat '$output_log' 2>&1
         #end if
     ]]></token>
     <xml name="in_log">
@@ -216,11 +216,15 @@
         </expand>
     </xml>
 
-    <!-- fastq input (used in denovomap, tsv2bam, ustacks) -->
-    <xml name="fastq_input" token_fastq_optional="false" token_help="">
+    <!-- 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 -->
+    <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help="">
         <conditional name="input_type">
             <param name="input_type_select" type="select" label="Short read data from individuals" help="@HELP@">
-                <option value="single" selected="true">single end or forward reads</option>
+                <option value="single" selected="true">@SE_OPTION@</option>
                 <option value="paired">(paired) dataset list</option>
             </param>
             <when value="single">
diff -r 3680074758c5 -r dddd1a6454ce stacks_denovomap.xml
--- a/stacks_denovomap.xml	Thu Jun 20 08:14:41 2019 -0400
+++ b/stacks_denovomap.xml	Tue Jun 25 10:59:31 2019 -0400
@@ -9,7 +9,6 @@
 @FASTQ_INPUT_FUNCTIONS@
 mkdir stacks_inputs stacks_outputs&&
 
-
 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, ".%d" )
 $link_command
 
@@ -25,7 +24,12 @@
 -n $assembly_options.n
 --var-alpha $model_options.var_alpha
 --gt-alpha $model_options.gt_alpha
-$paired
+#if $input_type.input_type_select == "paired"
+    --paired
+#end if
+$pe_options.rm_pcr_duplicates
+--min-samples-per-pop $popfilter_options.min_samples_per_pop
+--min-populations $popfilter_options.min_populations
 
 ## the catalog.calls output is a gzip-ed vcf extract it
 ## to make it usable in Galaxy (with the downside that we
@@ -41,10 +45,16 @@
             <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual" help="used in ustacks"/>
             <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog" help="used in cstacks; suggested: set to -M"/>
         </section>
-        <section name="model_options" title="Variant calling options (for gstacks)" expanded="true">
+        <section name="model_options" title="SNP model options" expanded="true">
             <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
         </section>
-        <param argument="--paired" type="boolean" checked="false" truevalue="--paired" falsevalue="" label="Use paired-end reads to assemble mini-contigs" help="After assembling RAD loci (in the tsv2bam step)" />
+		<section name="pe_options" title="Paired-end options" expanded="true">
+            <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="remove all but one set of read pairs of the same sample that have the same insert length" help="" />
+        </section>
+		<section name="popfilter_options" title="Population filtering options" expanded="true">
+            <param argument="--min-samples-per-pop" name="min_samples_per_pop" type="integer" value="0" label="minimum percentage of individuals in a population required to process a locus for that population" help="(for populations; default: 0)"/>
+            <param argument="--min-populations" name="min_populations" type="integer" value="1" label="minimum number of populations a locus must be present in to process a locus" help="(for populations; default: 1)" />
+        </section>
         <expand macro="in_log"/>
     </inputs>
     <outputs>
@@ -82,7 +92,6 @@
                 </collection>
             </param>
             <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
-            <param name="paired" value="--paired" />
             <output_collection name="tabs" count="6">
                 <element name="PopA_01.tags" file="ustacks/PopA_01.tags.tsv" ftype="tabular" lines_diff="2"/>
                 <element name="PopA_01.snps" file="ustacks/PopA_01.snps.tsv" ftype="tabular" lines_diff="2"/>
@@ -146,11 +155,17 @@
             <param name="assembly_options|n" value="3" />
             <param name="model_options|var_alpha" value="0.1" />
             <param name="model_options|gt_alpha" value="0.1" />
+            <param name="pe_options|rm_pcr_duplicates" value="--rm-pcr-duplicates" />
+            <param name="popfilter_options|min_samples_per_pop" value="1"/>
+            <param name="popfilter_options|min_populations" value="0" />
             <assert_command>
                 <has_text text="-M 3" />
                 <has_text text="-n 3" />
                 <has_text text="\-\-var-alpha 0.1" />
                 <has_text text="\-\-gt-alpha 0.1" />
+                <has_text text="\-\-rm-pcr-duplicates" />
+                <has_text text="\-\-min-samples-per-pop 1" />
+                <has_text text="\-\-min-populations 0" />
             </assert_command>
             <output_collection name="tabs" count="6"/>
             <output_collection name="catalog" type="list" count="3"/>
@@ -164,38 +179,6 @@
             <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
             <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output>
         </test>
-        <!-- paired input, deafults (not using reverse reads), testing against the output of the pipeline components (note, this is equal because reverse reads are not used) -->
-        <test>
-            <param name="input_type|input_type_select" value="paired"/>
-            <param name="input_type|fqinputs">
-                <collection type="list:paired">
-                    <element name="PopA_01">
-                        <collection type="paired">
-                            <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
-                            <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
-                        </collection>
-                    </element>
-                    <element name="PopA_02">
-                        <collection type="paired">
-                            <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
-                            <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
-                        </collection>
-                    </element>
-                </collection>
-            </param>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
-            <output_collection name="tabs" count="6"/>
-            <output_collection name="catalog" type="list" count="3"/>
-            <output_collection name="matches" type="list" count="2"/>
-            <output_collection name="bams" type="list" count="2"/>
-            <output_collection name="gstacks_out" type="list" count="2"/>
-            <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output>
-            <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output>
-            <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
-            <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output>
-            <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
-            <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output>
-        </test>
     </tests>
 
     <help>
diff -r 3680074758c5 -r dddd1a6454ce test-data/.gentest.sh.swp
Binary file test-data/.gentest.sh.swp has changed