Mercurial > repos > bgruening > bionano_scaffold

diff bionano_scaffold.xml @ 8:5258e18bbe23 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 25785fac3064e7def7ebccd45d452dc0b22ec89a"
author bgruening
date Sat, 05 Feb 2022 18:15:29 +0000
parents a7f16f24e9a1
children faee8629b460
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line diff
--- a/bionano_scaffold.xml	Mon Jan 17 08:15:31 2022 +0000
+++ b/bionano_scaffold.xml	Sat Feb 05 18:15:29 2022 +0000
@@ -6,7 +6,7 @@
     <expand macro="edam_ontology"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-        #set RefAligner = '/usr/local/bin/RefAligner'
+        #set RefAligner = '/RefAligner/RefAligner'
         #set output_file_NCBI = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta'
         #set output_file_not_scaffolded = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta'
         ## softlinks do not work
@@ -56,6 +56,7 @@
         $zip_file
         -o ./
         #if $trim_cut_sites
+            && export PATH=/opt/conda/bin/:\$PATH
             && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log'
             && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log'
         #end if 
@@ -472,7 +473,6 @@
             </output>            
             <output name="results" ftype="zip">
                 <assert_contents>
-                    <!--<has_size value="4231746" delta="300" />-->
                     <has_archive_member path=".*/status.txt"/>
                 </assert_contents>
             </output>
@@ -540,7 +540,6 @@
             </assert_stdout>
             <assert_stdout>
                 <has_text text="hybridScaffold"/>
-                <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/-->
             </assert_stdout>
         </test>
         <test expect_num_outputs="6">
@@ -581,7 +580,6 @@
             </output>            
             <output name="results" ftype="zip">
                 <assert_contents>
-                    <!--<has_size value="4231908" delta="300" />-->
                     <has_archive_member path=".*/status.txt"/>
                 </assert_contents>
             </output>