Profile version update and minor fixes

galaxyproject · Nov 25, 2024 · a529d26 · a529d26
1 parent 908a0f4
commit a529d26
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Showing 2 changed files with 15 additions and 18 deletions.
diff --git a/tools/hicstuff/hicstuff_pipeline.xml b/tools/hicstuff/hicstuff_pipeline.xml
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 hicstuff pipeline 
     --genome '$genome' 
@@ -79,10 +79,10 @@ hicstuff pipeline
     </outputs>
     <tests>
         <test expect_num_outputs="3">
-            <param name="genome" value="seq.fa.gz" />
+            <param name="genome" value="seq.fa.gz"/>
             <param name="paired_cond|paired_select" value="separate"/>
-            <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" />
-            <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz" />
+            <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz"/>
+            <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz"/>
             <output name="abs_fragments_contacts_weighted_graal">
                 <assert_contents>
                     <has_n_lines n="77"/>
@@ -97,15 +97,15 @@ hicstuff pipeline
             </output>
             <output name="info_contigs" file="info_contigs.txt"/>
             <assert_stderr>
-                <has_text text="Contact map generated" />
+                <has_text text="Contact map generated"/>
             </assert_stderr>
         </test>
         <!-- bg2 format -->
         <test expect_num_outputs="3">
-            <param name="genome" value="seq.fa.gz" />
+            <param name="genome" value="seq.fa.gz"/>
             <param name="paired_cond|paired_select" value="separate"/>
-            <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" />
-            <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz" />
+            <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz"/>
+            <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz"/>
             <param name="matfmt" value="bg2"/>
             <output name="abs_fragments_contacts_weighted_bg2">
                 <assert_contents>
@@ -121,15 +121,15 @@ hicstuff pipeline
             </output>
             <output name="info_contigs" file="info_contigs.txt"/>
             <assert_stderr>
-                <has_text text="Contact map generated" />
+                <has_text text="Contact map generated"/>
             </assert_stderr>
         </test>
         <!-- cool format -->
         <test expect_num_outputs="3">
-            <param name="genome" value="seq.fa.gz" />
+            <param name="genome" value="seq.fa.gz"/>
             <param name="paired_cond|paired_select" value="separate"/>
-            <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" />
-            <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz" />
+            <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz"/>
+            <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz"/>
             <param name="matfmt" value="cool"/>
             <output name="abs_fragments_contacts_weighted_cool">
                 <assert_contents>
@@ -144,7 +144,7 @@ hicstuff pipeline
             </output>
             <output name="info_contigs" file="info_contigs.txt"/>
             <assert_stderr>
-                <has_text text="Contact map generated" />
+                <has_text text="Contact map generated"/>
             </assert_stderr>
         </test>
     </tests>
@@ -170,5 +170,5 @@ Output files
 * Contig info.txt: Contains chromosome names, theirs length and number of bins.
 
     ]]></help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>
diff --git a/tools/hicstuff/macros.xml b/tools/hicstuff/macros.xml
@@ -1,12 +1,9 @@
 <macros>
     <token name="@TOOL_VERSION@">3.2.4</token><!-- TODO remove cooler and biopython requirement on update -->
-    <token name="@PROFILE@">21.09</token>
+    <token name="@PROFILE@">23.02</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">hicstuff</requirement>
-            <requirement type="package" version="0.10.2">cooler</requirement>
-            <requirement type="package" version="1.84">biopython</requirement>
-            <yield/>
         </requirements>
     </xml>
     <xml name="citations">