Omark fixes (galaxyproject#5815)

bebatut · Mar 7, 2024 · 839a3c8 · 839a3c8
1 parent 67067cd
commit 839a3c8
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Showing 4 changed files with 22 additions and 14 deletions.
diff --git a/tools/omark/macros.xml b/tools/omark/macros.xml
@@ -1,5 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.3.0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
 
     <xml name="requirements">
         <requirement type="package" version="@TOOL_VERSION@">omark</requirement>
@@ -8,7 +9,7 @@
 
     <xml name="citation">
         <citations>
-            <citation type="doi">10.1101/2022.11.25.517970</citation> 
+            <citation type="doi">10.1101/2022.11.25.517970</citation>
         </citations>
     </xml>
 

diff --git a/tools/omark/omark.xml b/tools/omark/omark.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="omark" name="OMArk" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+<tool id="omark" name="OMArk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>proteome quality assessment</description>
     <macros>
         <import>macros.xml</import>
@@ -9,24 +9,25 @@
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
-    omamer search --db '$database' --query '$input' --out 'output_omamer'
+    omamer search --db '$database.fields.path' --query '$input' --out 'output_omamer'
+
     &&
 
     omark
     -f 'output_omamer'
-    -d '$database'
+    -d '$database.fields.path'
     $omark_mode
     -i '$input_iso'
-    -t 't'
-    -r 'r'
+    -t '$t'
+    -r '$r'
     -o omark_galaxy
 
     ]]></command>
 
     <inputs>
         <param name="input" type="data" format="fasta" label="Protein sequences"/>
         <param name="input_iso" type="data" format="txt" optional="true" label="Input isoform file" help="A semi-colon separated file, listing all isoforms of each genes, with one gene per line."/>
-        <param argument="-c" name="omark_mode" type="boolean" checked="false" label="Only compute a list of conserved HOGs" help="Can be used to obtain a set of genes on which to train"/>
+        <param argument="-c" name="omark_mode" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Only compute a list of conserved HOGs" help="Can be used to obtain a set of genes on which to train"/>
         <param name="database" label="OMAmer database" type="select">
             <options from_data_table="omamer"/>
         </param>
@@ -47,7 +48,7 @@
             </sanitizer>
             <validator type="regex">[0-9a-zA-Z_]+</validator>
         </param>
-        
+
         <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
             <option value="detail_sum" selected="true">Detailed summary</option>
             <option value="hog">HOG identifiers</option>
@@ -88,15 +89,21 @@
             <param name="input" value="input.fasta"/>
             <param name="outputs" value="sum,detail_sum,png,hog,pdf,ump,tax"/>
             <param name="database" value="test"/>
+
+            <!-- Couldn't create a minimal working hdf5 dataset -->
+            <assert_stderr>
+                <has_text text="file signature not found"/>
+                <has_text text="End of HDF5 error back trace" />
+            </assert_stderr>
         </test>
     </tests>
 
 
     <help><![CDATA[
-        OMark_: is a software for proteome quality assessment. 
+        OMark_: is a software for proteome quality assessment.
         It provides measures of proteome completeness, characterizes the consistency
         of all protein coding genes with regard to their homologs, and identifies the
-        presence of contamination from other species. 
+        presence of contamination from other species.
 
         OMArk relies on the OMA orthology database.
         For more information, please refer to the OMamer_ documentaion.
@@ -105,4 +112,4 @@
         .. _OMamer: https://github.com/DessimozLab/omamer
     ]]></help>
     <expand macro="citation"/>
-</tool>
+</tool>
diff --git a/tools/omark/test-data/omamer.loc b/tools/omark/test-data/omamer.loc
@@ -2,5 +2,5 @@
 # - value
 # - name
 # - version
-# - /path/to/data 
-test    test	2.0.2	${__HERE__}/db/
+# - /path/to/data
+test	test	2.0.2	${__HERE__}/db/test.h5
diff --git a/tools/omark/tool-data/omamer.loc.sample b/tools/omark/tool-data/omamer.loc.sample
@@ -6,4 +6,4 @@
 #value  description version /path/to/data
 #
 #for example
-#Primates-v2.0    Primates	2.0.2	/path/to/data
+#Primates-v2.0	Primates	2.0.2	/path/to/data