Mercurial > repos > eduardo > meme_chip

diff meme_chip_wrapper.xml @ 9:89eab5bd597e draft default tip

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planemo upload
author eduardo
date Mon, 20 Feb 2017 14:02:55 -0500
parents 9fa889764fa5
children
line wrap: on
line diff
--- a/meme_chip_wrapper.xml	Mon Feb 20 13:41:31 2017 -0500
+++ b/meme_chip_wrapper.xml	Mon Feb 20 14:02:55 2017 -0500
@@ -5,7 +5,7 @@
     </requirements>
     <description></description>
     <version_command>echo "MEME version r4.10.0"</version_command>
-    <command> meme-chip $input_file -o ${memechip_out.files_path}
+    <command> meme-chip $input_file -o ${html_outfile.files_path}
         -db $__tool_directory__/JASPAR_CORE_2016.meme
         #if str( $options_type.options_type_selector ) == 'advanced':
             #if str( $options_type.bg_type.bg_type_selector) == 'bg_user':
@@ -77,11 +77,11 @@
         #end if
         <!--pipe stderr to stdout because of annoying log4perl warnings. Error when exit status-->
         2&gt;&amp;1 || echo "Error running MEME."
-        <!--&amp;&amp; mv ${html_outfile.files_path}/index.html ${html_outfile}-->
-        <!--&amp;&amp; zip -r result $html_outfile.files_path-->
-        &amp;&amp; cd ${memechip_out.files_path}
+        &amp;&amp; mv ${html_outfile.files_path}/index.html ${html_outfile}
+        &amp;&amp; zip -r result $html_outfile.files_path
+        <!--&amp;&amp; cd ${memechip_out.files_path}
         &amp;&amp; zip -rp memechip_out ./
-        &amp;&amp; mv memechip_out.zip ${memechip_out}
+        &amp;&amp; mv memechip_out.zip ${memechip_out}-->
     </command>
     <inputs>
         <param format="fasta" name="input_file" type="data" label="Sequences in fasta format" />
@@ -158,9 +158,9 @@
         </conditional>
     </inputs>
     <outputs>
-        <!--<data format="html" name="html_outfile" label="index" />-->
+        <data format="html" name="html_outfile" label="index" />
         <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
-        <data format="zip" name="memechip_out" label="SAVE ME ${tool.name} on #echo os.path.splitext(str($input_file.name))[0]#.zip" />
+        <!--<data format="zip" name="memechip_out" label="SAVE ME ${tool.name} on #echo os.path.splitext(str($input_file.name))[0]#.zip" />-->
     </outputs>