# HG changeset patch
# User matthias
# Date 1546590730 18000
# Node ID 756e003f0eb1b97bbef7f599c75b30a83c02b502
# Parent  39d8294476aaaa1369f13d699d34713a42dc2c3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2

diff -r 39d8294476aa -r 756e003f0eb1 macros.xml
--- a/macros.xml	Tue Dec 18 12:55:07 2018 -0500
+++ b/macros.xml	Fri Jan 04 03:32:10 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 39d8294476aa -r 756e003f0eb1 stacks_shortreads.xml
--- a/stacks_shortreads.xml	Tue Dec 18 12:55:07 2018 -0500
+++ b/stacks_shortreads.xml	Fri Jan 04 03:32:10 2019 -0500
@@ -93,8 +93,8 @@
             <output name="output_log" file="shortreads/process_shortreads.out" compare="sim_size"/>
             <output_collection name="demultiplexed_paired" type="list:paired" count="40">
                 <element name="PopA_01">
-                    <element name="forward" value="shortreads/PopA_01.forward.fq.gz" ftype="fastqsanger.gz" />
-                    <element name="reverse" value="shortreads/PopA_01.reverse.fq.gz" ftype="fastqsanger.gz" />
+                    <element name="forward" value="shortreads/PopA_01.forward.fq.gz" ftype="fastqsanger.gz" compare="sim_size"/>
+                    <element name="reverse" value="shortreads/PopA_01.reverse.fq.gz" ftype="fastqsanger.gz" compare="sim_size"/>
                 </element>
             </output_collection>
             <output_collection name="remaining" type="list:paired" count="40">
diff -r 39d8294476aa -r 756e003f0eb1 todo.txt
--- a/todo.txt	Tue Dec 18 12:55:07 2018 -0500
+++ b/todo.txt	Fri Jan 04 03:32:10 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