Mercurial > repos > bgruening > antismash

diff antismash.xml @ 5:bc88856eddab draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit dc45770442ff516d6f3733e4bdb284be3163de67
author bgruening
date Tue, 05 Jul 2022 10:37:38 +0000
parents e78e25d3b4bd
children
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line diff
--- a/antismash.xml	Tue May 31 14:04:07 2022 +0000
+++ b/antismash.xml	Tue Jul 05 10:37:38 2022 +0000
@@ -23,6 +23,13 @@
             ln -s $genefinding_gff3 annotation.gff3 &&
         #end if
 
+        #if $sideload.file
+            #if $sideload.format == 'harmonize'
+                python '$__tool_directory__/harmonize2antismash.py' '$sideload.file' sideload.json &&
+            #else
+                ln -s '$sideload.file' sideload.json &&
+            #end if
+        #end if
 
         ## create html folder
         mkdir -p '$htmloutputfolder' &&
@@ -62,6 +69,10 @@
             --rre-cutoff $advanced_options.rre_cutoff
             --rre-minlength $advanced_options.rre_minlength
 
+            #if $sideload.file
+                --sideload 'sideload.json'
+            #end if
+
             input_tempfile.$file_extension &&
 
         ## copy all content to html folder
@@ -149,6 +160,14 @@
             <param argument="--rre-minlength" type="integer" min="0" max="100" value="50" label="RRE minlength" help="Minimum amino acid length of RRE domains. Default: 50" />
         </section>
 
+        <section name="sideload" title="Sideloading" help="Sideloading allows you to load external datasets into AntiSMASH">
+            <param argument="--sideload" name="file" type="data" format="json" optional="true" label="sideload json file" help="Sideload json file to add to your report" />
+            <param name="format" type="select" label="Sideload Format">
+                <option value="harmonize">hAMRonize summarize JSON</option>
+                <option value="native">AntiSMASH JSON</option>
+            </param>
+        </section>
+        
         <param name="outputs" type="select" multiple="true" label="Outputs">
             <option value="html" selected="True">HTML file</option>
             <option value="all">All results</option>
@@ -236,6 +255,23 @@
         </output>
     </test>
  
+        <test expect_num_outputs="1">
+            <param name="infile" value="sequence.fasta"/>
+            <section name="sideload">
+                <param name="format" value="native"/>
+                <param name="file" value="sideload.json"/>
+            </section>
+            <output name="html" file="index.4.html"/>
+        </test>
+
+        <test expect_num_outputs="1">
+            <param name="infile" value="sequence.fasta"/>
+            <section name="sideload">
+                <param name="format" value="harmonize"/>
+                <param name="file" value="harmonize.json"/>
+            </section>
+            <output name="html" file="index.5.html"/>
+        </test>
     </tests>
     <help>
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