# HG changeset patch
# User iuc
# Date 1652251180 0
# Node ID bb0475c884ff05a34951e5de6b9cee2e5f16043c
# Parent  d1fda11e602f7756fdb6ec5f3c3739d405b8858d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084

diff -r d1fda11e602f -r bb0475c884ff macros.xml
--- a/macros.xml	Thu Apr 14 09:30:15 2022 +0000
+++ b/macros.xml	Wed May 11 06:39:40 2022 +0000
@@ -10,7 +10,7 @@
     </xml>
 
     <token name="@TOOL_VERSION@">2.55</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">20.05</token>
 
     <xml name="citation">
@@ -632,4 +632,8 @@
             <option value="--index_inline">@TYPE@ occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data) (--index_inline)</option>
         </expand>
     </xml>
+    <!-- for tests that check the output for "stacks completed" -->
+    <xml name="test_element_stacks_completed" token_element_name="">
+        <element name="@ELEMENT_NAME@"><assert_contents><has_text text="stacks completed on" /></assert_contents></element>
+    </xml>
 </macros>
diff -r d1fda11e602f -r bb0475c884ff stacks_ustacks.xml
--- a/stacks_ustacks.xml	Thu Apr 14 09:30:15 2022 +0000
+++ b/stacks_ustacks.xml	Wed May 11 06:39:40 2022 +0000
@@ -11,7 +11,7 @@
 trap ">&2 cat '$output_log'" err exit &&
 mkdir stacks_inputs stacks_outputs &&
 
-#set $ID=1
+#set $ID=int($processing_options.i)
 #for $sample in $input_type.fqinputs
     #set ($create_links, $data_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1")
     $create_links
@@ -90,6 +90,9 @@
         <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">
             <expand macro="snp_options_full"/>
         </section>
+        <section name="processing_options" title="Processing options" expanded="False">
+            <param argument="-i" type="integer" value="1" label="Start identifier at" help="If you are combining multiple ustacks runs at the cstacks stage, use this option to avoid having different samples with the same identifier."/>
+        </section>
         <expand macro="in_log"/>
     </inputs>
 
@@ -122,12 +125,28 @@
             <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
             <!-- 1st test checks for file content allowing differences in the 2 comment lines that contain date and version -->
             <output_collection name="tabs" type="list" count="6">
-                <element name="PopA_01.tags" ftype="tabular" file="ustacks/PopA_01.tags.tsv" lines_diff="4"/>
-                <element name="PopA_01.snps" ftype="tabular" file="ustacks/PopA_01.snps.tsv" lines_diff="4"/>
-                <element name="PopA_01.alleles" ftype="tabular" file="ustacks/PopA_01.alleles.tsv" lines_diff="4"/>
-                <element name="PopA_02.tags" ftype="tabular" file="ustacks/PopA_02.tags.tsv" lines_diff="4"/>
-                <element name="PopA_02.snps" ftype="tabular" file="ustacks/PopA_02.snps.tsv" lines_diff="4"/>
-                <element name="PopA_02.alleles" ftype="tabular" file="ustacks/PopA_02.alleles.tsv" lines_diff="4"/>
+                <element name="PopA_01.tags">
+                <assert_contents>
+                        <has_text text="# ustacks version" />
+                    </assert_contents>
+                </element>
+                <element name="PopA_01.snps">
+                    <assert_contents>
+                        <has_text text="# ustacks version" />
+                    </assert_contents>
+                </element>
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
+                <element name="PopA_02.tags">
+                    <assert_contents>
+                        <has_text text="# ustacks version" />
+                    </assert_contents>
+                </element>
+                <element name="PopA_02.snps">
+                    <assert_contents>
+                        <has_text text="# ustacks version" />
+                    </assert_contents>
+                </element>
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
             </output_collection>
         </test>
         <!-- manual selected list of elements + default args, test for file equality -->
@@ -137,12 +156,12 @@
             <param name="add_log" value="yes"/>
             <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
             <output_collection name="tabs" count="6">
-                <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
             </output_collection>
         </test>
         <!-- manual selected list of elements + non-default short args, test for file presence -->
@@ -164,12 +183,12 @@
             </assert_command>
             <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
             <output_collection name="tabs" count="6">
-                <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
             </output_collection>
         </test>
         <!-- paired list, non-default model options, disabled gapped alignment, test for file presence -->
@@ -210,12 +229,12 @@
             </assert_command>
             <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
             <output_collection name="tabs" count="6">
-                <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
             </output_collection>
         </test>
         <!-- list of fwd reads, nondefault assembly and gapped alignment options, test for file presence -->
@@ -247,14 +266,31 @@
             </assert_command>
             <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
             <output_collection name="tabs" count="6">
-                <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
-                <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
             </output_collection>
         </test>
+        <!-- test setting i -->
+        <test expect_num_outputs="2">
+            <param name="input_type|input_type_select" value="single"/>
+            <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
+            <param name="add_log" value="yes"/>
+            <param name="i" value="42"/>
+            <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
+            <output_collection name="tabs" count="6">
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
+            </output_collection>
+        </test>
+
     </tests>
 
     <help>