# HG changeset patch
# User matthias
# Date 1546590678 18000
# Node ID 61afc5a3cd8e76cb53fd2a46fb574ea9d752c64d
# Parent  8427e904f35280cfcac90b6022630e015838886f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2

diff -r 8427e904f352 -r 61afc5a3cd8e macros.xml
--- a/macros.xml	Tue Dec 18 12:52:48 2018 -0500
+++ b/macros.xml	Fri Jan 04 03:31:18 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 8427e904f352 -r 61afc5a3cd8e stacks_cstacks.xml
--- a/stacks_cstacks.xml	Tue Dec 18 12:52:48 2018 -0500
+++ b/stacks_cstacks.xml	Fri Jan 04 03:31:18 2019 -0500
@@ -19,7 +19,7 @@
 ## - create -s sample1prefix -s sample2prefix .. 
 
 #set $samples = ""
-#for $input_file in $input_col
+#for $input_file in $input_cat
     #set $filename = str($input_file.element_identifier)
     #if not filename.endswith('.tsv')
         #set $filename = $filename + ".tsv"
@@ -66,7 +66,7 @@
     ]]></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, refmap, ustacks or pstacks)" />
+	<expand macro="input_cat_macro"/>
 
         <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, the catalog will be built from samples listed in this file" optional="true" argument="-M" />
 
@@ -87,7 +87,7 @@
         <!-- TODO add test w popmap -->
         <!-- test w default options -->
         <test>
-            <param name="input_col">
+            <param name="input_cat">
                 <collection type="list">
                     <element name="PopA_01.alleles.tsv" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
                     <element name="PopA_01.snps.tsv" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
@@ -107,7 +107,7 @@
         </test>
         <!-- test w non default options (wo gapped, because tested already in ustacks) -->
         <test>
-            <param name="input_col">
+            <param name="input_cat">
                 <collection type="list">
                     <element name="PopA_01.alleles.tsv" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
                     <element name="PopA_01.snps.tsv" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
@@ -140,13 +140,13 @@
 
 **What it does**
 
-A catalog can be built from any set of samples processed by the ustacks or pstacks programs. It will create a set of consensus loci, merging alleles together. In the case of a genetic cross, a catalog would be constructed from the parents of the cross to create a set of all possible alleles expected in the progeny of the cross.
+A catalog can be built from any set of samples processed by ustacks. It will create a set of consensus loci, merging alleles together. In the case of a genetic cross, a catalog would be constructed from the parents of the cross to create a set of all possible alleles expected in the progeny of the cross.
 
 --------
 
 **Input files**
 
-Output from denovo_map, refmap, ustacks or pstacks
+Output from denovo_map, refmap, or ustacks
 
 **Output files**
 
diff -r 8427e904f352 -r 61afc5a3cd8e todo.txt
--- a/todo.txt	Tue Dec 18 12:52:48 2018 -0500
+++ b/todo.txt	Fri Jan 04 03:31:18 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