fix test. Now evreything is done just wait till datatype is up

galaxyproject · Dec 20, 2024 · 6a9629b · 6a9629b
1 parent 9071a35
commit 6a9629b
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Showing 2 changed files with 14 additions and 11 deletions.
diff --git a/tools/fairy/fairy_cov.xml b/tools/fairy/fairy_cov.xml
@@ -7,16 +7,19 @@
     <command detect_errors="exit_code">
         <![CDATA[
 
+            ln -s '$contig' '$contig.element_identifier' &&
+            ln -s '$bcsp_file' '$bcsp_file.element_identifier' &&
+
             fairy coverage
-            '$contig'
-            '$bcsp'
+            '$contig.element_identifier'
+            '$bcsp_file.element_identifier'
             -t \${GALAXY_SLOTS:-8}
-            -m ${minimum-ani}
-            -M ${min-number-kmers}
+            -m ${minimum_ani}
+            -M ${min_number_kmers}
             -c ${c}
             -k ${k.value}
-            --min-spacing ${min-spacing}
-            ${full-contig-name}
+            --min-spacing ${min_spacing}
+            ${full_contig_name}
             #if $output_type.value == 'semi':
                 --aemb-format
             #end if
@@ -29,7 +32,7 @@
     </command>
     <inputs>
         <param name="contig" type="data" format="fasta,fasta.gz" label="Input fasta contig file" help="Input the raw fasta contig file. It can be gzip!"/>
-        <param name="bcsp" type="data" format="bcsp" label="Input the pre-sketched file (.bcsp file)" help="This file will be generated with the fairy sketch tool."/>
+        <param name="bcsp_file" type="data" format="bcsp" label="Input the pre-sketched file (.bcsp file)" help="This file will be generated with the fairy sketch tool."/>
         <param argument="--minimum-ani" type="integer" optional="true" min="0" max="100" value="95" label="Set minimum ANI" help="Set the minimum adjusted ANI for the coverage calculation. CARE: only adjust it when you know what it does!"/>
         <param argument="--min-number-kmers" type="integer" value="8" optional="true" label="Genome filter" help="Set the number for exclude genomes with less than this number of sampled k-mers."/>
         <param argument="-c" type="integer" value="50" optional="true" label="Set subsampling rate" help="This value does not interact with the .bcsp file which was used as input."/>
@@ -51,12 +54,12 @@
     <tests>
         <test>
             <param name="contig" value="single_test.fasta.gz" ftype="fasta.gz"/>
-            <param name="bcsp" value="single_test.fasta.gz.bcsp" ftype="bcsp"/>
+            <param name="bcsp_file" value="single_test.fasta.gz.bcsp" ftype="bcsp"/>
             <output name="output" value="normal_test.tsv"/>
         </test>
         <test>
             <param name="contig" value="single_test.fasta.gz" ftype="fasta.gz"/>
-            <param name="bcsp" value="single_test.fasta.gz.bcsp" ftype="bcsp"/>
+            <param name="bcsp_file" value="single_test.fasta.gz.bcsp" ftype="bcsp"/>
             <param name="minimum-ani" value="99"/>
             <param name="min-number-kmers" value="2"/>
             <param name="full-contig-name" value="true"/>
@@ -65,7 +68,7 @@
         </test>
         <test>
             <param name="contig" value="single_test.fasta.gz" ftype="fasta.gz"/>
-            <param name="bcsp" value="single_test.fasta.gz.bcsp" ftype="bcsp"/>
+            <param name="bcsp_file" value="single_test.fasta.gz.bcsp" ftype="bcsp"/>
             <param name="k" value="21"/>
             <param name="c" value="45"/>
             <param name="min-spacing" value="10"/>

diff --git a/tools/fairy/test-data/test_2.tsv b/tools/fairy/test-data/test_2.tsv
@@ -1 +1 @@
-NZ_CP017438.1 Escherichia coli O157:H7 strain 2159 chromosome, complete genome	0.05509718146076748
+NZ_CP017438.1	0.05509718146076748
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		NZ_CP017438.1 Escherichia coli O157:H7 strain 2159 chromosome, complete genome 0.05509718146076748
		NZ_CP017438.1 0.05509718146076748