Mercurial > repos > iuc > stacks2_denovomap

changeset 6:89eb29319bf4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
author iuc
date Wed, 11 May 2022 06:50:13 +0000
parents 04db7fd6b238
children 33486216eec0
files macros.xml stacks_denovomap.xml
diffstat 2 files changed, 88 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Apr 14 09:20:20 2022 +0000
+++ b/macros.xml	Wed May 11 06:50:13 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>
--- a/stacks_denovomap.xml	Thu Apr 14 09:20:20 2022 +0000
+++ b/stacks_denovomap.xml	Wed May 11 06:50:13 2022 +0000
@@ -96,36 +96,100 @@
             </param>
             <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
             <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output>
-            <output_collection name="tabs" count="6">
-                <element name="PopA_01.tags" file="ustacks/PopA_01.tags.tsv" ftype="tabular" lines_diff="4"/>
-                <element name="PopA_01.snps" file="ustacks/PopA_01.snps.tsv" ftype="tabular" lines_diff="4"/>
-                <element name="PopA_01.alleles" file="ustacks/PopA_01.alleles.tsv" ftype="tabular" lines_diff="4"/>
-                <element name="PopA_02.tags" file="ustacks/PopA_02.tags.tsv" ftype="tabular" lines_diff="4"/>
-                <element name="PopA_02.snps" file="ustacks/PopA_02.snps.tsv" ftype="tabular" lines_diff="4"/>
-                <element name="PopA_02.alleles" file="ustacks/PopA_02.alleles.tsv" ftype="tabular" lines_diff="4"/>
+            <output_collection name="tabs" type="list" count="6">
+                <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>
             <output_collection name="catalog" type="list" count="3">
-                <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="4"/>
-                <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="4"/>
-                <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="4"/>
+                <element name="catalog.alleles">
+                    <assert_contents>
+                        <has_text text="# cstacks version " />
+                    </assert_contents>
+                </element>
+                <element name="catalog.snps" >
+                    <assert_contents>
+                        <has_text text="# cstacks version" />
+                    </assert_contents>
+                </element>
+                <element name="catalog.tags">
+                    <assert_contents>
+                        <has_text text="# cstacks version" />
+                    </assert_contents>
+                </element>
             </output_collection>
             <output_collection name="matches" type="list" count="2">
-                <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="4"/>
-                <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="4"/>
+                <element name="PopA_01.matches">
+                    <assert_contents>
+                        <has_text text="# sstacks version" />
+                    </assert_contents>
+                </element>
+                <element name="PopA_02.matches" >
+                    <assert_contents>
+                        <has_text text="# sstacks version" />
+                    </assert_contents>
+                </element>
             </output_collection>
             <output_collection name="bams" type="list" count="2">
-                <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
-                <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/>
+                <element name="PopA_01.matches">
+                    <assert_contents>
+                        <has_size value="1153" delta="200" />
+                    </assert_contents>
+                </element>
+                <element name="PopA_02.matches" >
+                    <assert_contents>
+                        <has_size value="1169" delta="200" />
+                    </assert_contents>
+                </element>
             </output_collection>
             <output_collection name="gstacks_out" type="list" count="2">
-                <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="4"/>
-                <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="diff"/>
+                <element name="catalog.calls.vcf">
+                    <assert_contents>
+                        <has_text text="##fileformat=VCFv4.2" />
+                    </assert_contents>
+                </element>
+                <element name="catalog.fa.gz" >
+                    <assert_contents>
+                        <has_size value="334" delta="100" />
+                    </assert_contents>
+                </element>
             </output_collection>
-            <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
-            <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv" compare="diff"/>
+            <output name="out_haplotypes">
+                <assert_contents>
+                    <has_text_matching expression="\#\s+Catalog\s+Locus\s+ID\s+Cnt" />
+                </assert_contents>
+            </output>
+            <output name="out_hapstats">
+                <assert_contents>
+                    <has_text_matching expression="\#\s+Locus\s+ID\s+Chr\s+BP" />
+                </assert_contents>
+            </output>
             <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
             <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
-            <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
+            <output name="out_sumstats">
+                <assert_contents>
+                    <has_text_matching expression="\#\s+Locus\s+ID\s+Chr\s+BP" />
+                </assert_contents>
+            </output>
         </test>
         <!-- SE input as multi selection, defaults testing against the output of the pipeline components -->
         <test expect_num_outputs="11">