# HG changeset patch
# User matthias
# Date 1546591036 18000
# Node ID cc87f9d30171061159347a840e9acc8d2affcebe
# Parent  d530aff416bdc1a06a01c9e819563b4d3370a08e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2

diff -r d530aff416bd -r cc87f9d30171 macros.xml
--- a/macros.xml	Tue Dec 18 13:04:09 2018 -0500
+++ b/macros.xml	Fri Jan 04 03:37:16 2019 -0500
@@ -128,6 +128,20 @@
         </data>
     </xml>
 
+    <!-- inputs from previous pipeline steps -->
+    <xml name="input_cat_macro">
+        <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" />
+    </xml>
+    <xml name="input_tags_macro">
+        <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks" />
+    </xml>
+    <xml name="input_matches_macro">
+        <param name="input_matches" format="tabular,txt" type="data_collection" collection_type="list" label="Matches to the catalog" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or sstacks" />
+    </xml>
+    <xml name="input_aln_macro">
+        <param name="input_aln" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" />
+    </xml>
+
 
     <!-- fastq input -->
     <xml name="fastq_input_macro" token_fastq_optional="false">
@@ -241,9 +255,9 @@
     </xml>
 
     <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) -->
-    <!-- TODO tags, snps, and alleles could go to sub collections -->
+    <!-- TODO tags, snps, and alleles could go to sub collections; same for other tools -->
     <xml name="ustacks_outputs_macro" token_tooladd="">
-        <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Stacks">
+        <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci per sample">
             <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
             <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
             <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
@@ -251,7 +265,7 @@
     </xml>
     <!-- cstacks outputs collection containing catalog.tags.tsv, catalog.snps.tsv, catalog.alleles.tsv -->
     <xml name="cstacks_outputs_macro" token_tooladd="">
-        <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog">
+        <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog of loci">
             <discover_datasets pattern="(?P&lt;name&gt;catalog\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
     </xml>
@@ -263,13 +277,13 @@
     </xml>
     <!-- tsv2bam outputs collection containing SAMPLE.matches.bam -->
     <xml name="tsv2bam_outputs_macro" token_tooladd="">
-        <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Stacks">
+        <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci">
             <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.bam$" ext="bam" directory="stacks_outputs" />
         </collection>
     </xml>
     <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz -->
     <xml name="gstacks_outputs_macro" token_tooladd="">
-        <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string}">
+        <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites">
             <discover_datasets pattern="(?P&lt;name&gt;catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs" />
             <discover_datasets pattern="(?P&lt;name&gt;catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs" />
         </collection>
diff -r d530aff416bd -r cc87f9d30171 stacks_populations.xml
--- a/stacks_populations.xml	Tue Dec 18 13:04:09 2018 -0500
+++ b/stacks_populations.xml	Fri Jan 04 03:37:16 2019 -0500
@@ -13,7 +13,7 @@
 &&
 
 #if str($options_usage.input_type) == 'stacks'
-    #for $input_file in $options_usage.input_col
+    #for $input_file in $options_usage.input_aln
         #set $filename = str($input_file.element_identifier)
         #if $filename == "catalog.calls" or $filename == "catalog.fa.gz":
             ln -s '${input_file}' 'stacks_inputs/${filename}' &&
@@ -151,7 +151,7 @@
                 <option value="vcf">VCF file</option>
             </param>
             <when value="stacks">
-                <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" />
+                <expand macro="input_aln_macro"/>
             </when>
             <when value="vcf">
                 <param name="input_vcf" format="vcf" type="data" label="VCF file" argument="-V" />
@@ -296,7 +296,7 @@
         <!-- test w gstacks output as input and default options -->
         <test>
             <param name="options_usage|input_type" value="stacks" />
-            <param name="options_usage|input_col">
+            <param name="options_usage|input_aln">
                 <collection type="list">
                     <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
                     <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
@@ -315,7 +315,7 @@
         <!-- test w gstacks output as input, wo popmap, and default options -->
         <test>
             <param name="options_usage|input_type" value="stacks" />
-            <param name="options_usage|input_col">
+            <param name="options_usage|input_aln">
                 <collection type="list">
                     <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
                     <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
@@ -327,7 +327,7 @@
         <!-- test w gstacks output as input and + all outputs -->
         <test>
             <param name="options_usage|input_type" value="stacks" />
-            <param name="options_usage|input_col">
+            <param name="options_usage|input_aln">
                 <collection type="list">
                     <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
                     <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
@@ -388,7 +388,7 @@
         <!-- test w gstacks output as input and non default filtering -->
         <test>
             <param name="options_usage|input_type" value="stacks" />
-            <param name="options_usage|input_col">
+            <param name="options_usage|input_aln">
                 <collection type="list">
                     <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
                     <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
@@ -419,7 +419,7 @@
         <!-- test w gstacks output as input and non default merging/hwe -->
         <test>
             <param name="options_usage|input_type" value="stacks" />
-            <param name="options_usage|input_col">
+            <param name="options_usage|input_aln">
                 <collection type="list">
                     <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
                     <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
@@ -446,7 +446,7 @@
         <!-- test w gstacks output as input and non default fstats/kernel/bootstrap -->
         <test>
             <param name="options_usage|input_type" value="stacks" />
-            <param name="options_usage|input_col">
+            <param name="options_usage|input_aln">
                 <collection type="list">
                     <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
                     <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
@@ -487,7 +487,7 @@
 
     <!--        <test>
             <param name="options_usage|input_type" value="stacks" />
-            <param name="options_usage|input_col">
+            <param name="options_usage|input_aln">
                 <collection type="list">
                     <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
                     <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
diff -r d530aff416bd -r cc87f9d30171 todo.txt
--- a/todo.txt	Tue Dec 18 13:04:09 2018 -0500
+++ b/todo.txt	Fri Jan 04 03:37:16 2019 -0500
@@ -7,8 +7,7 @@
 
 Raw Reads
     process_radtags planemo test-data-generated-wdefaults sufficient-test
-    process_shortreads
-        parameters 
+    process_shortreads parameters "
     clone_filter
         parameters
     kmer_filter