Merge pull request #6562 from hugolefeuvre/groot_update

Groot modification
galaxyproject · Nov 14, 2024 · fcdb311 · fcdb311
2 parents dc0a3f2 + 95a69c8
commit fcdb311
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Showing 2 changed files with 4 additions and 95 deletions.
diff --git a/tools/groot/groot.xml b/tools/groot/groot.xml
@@ -2,7 +2,7 @@
     <description> align reads to references and weight variation graphs and generate report</description>
     <macros>
         <token name="@TOOL_VERSION@">1.1.2</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <token name="@PROFILE@">22.05</token>
     </macros>
     <xrefs>
@@ -13,7 +13,7 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 set -x pipefail;
-#set $extension = str($fastq.ext)
+#set $extension = "fastq.gz" if str($fastq.ext).endswith(".gz") else "fastq"
 ln -s -f '${fastq}' 'input.${extension}' &&
 groot index
     --msaDir '$groot_db_select.fields.path'
@@ -31,7 +31,6 @@ groot align
     --indexDir 'grootIndex'
     --contThresh $contThresh
     --minKmerCov $minKmerCov
-    --log '$log'
     $noAlign
     --processors "\${GALAXY_SLOTS:-1}"
 
@@ -69,11 +68,10 @@ groot align
         </section>
     </inputs>
     <outputs>
-        <data name="log" format="txt" label="${tool.name} on ${on_string}: Log"/>
         <data name="report_out" format="tabular" label="${tool.name} on ${on_string}: Report"/>
     </outputs>
     <tests>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="1">
             <param name="fastq" value="bla-b7-150bp-5x.fq" ftype="fastq"/>
             <section name="index">
                 <param name="groot_db_select" value="resfinder.90" />
@@ -102,14 +100,8 @@ groot align
                     <has_n_columns n="4"/>
                 </assert_contents>
             </output>
-            <output name="log" ftype="txt">
-                <assert_contents>
-                    <has_text text="version"/>
-                    <has_text text="1.1.2"/>
-                </assert_contents>
-            </output>
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="1">
             <param name="fastq" value="argannot_light-150bp-10000-reads.fq.gz" ftype="fastq.gz"/>
             <section name="index">
                 <param name="groot_db_select" value="arg-annot.90" />
@@ -137,12 +129,6 @@ groot align
                     <has_n_columns n="4"/>
                 </assert_contents>
             </output>
-            <output name="log" ftype="txt">
-                <assert_contents>
-                    <has_text text="version"/>
-                    <has_text text="1.1.2"/>
-                </assert_contents>
-            </output>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/groot/test-data/groot.log b/tools/groot/test-data/groot.log