diff macros.xml @ 0:559e11a57c3e draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Oct 20 04:34:18 2017 -0400
@@ -0,0 +1,86 @@
+<macros>
+    <token name="@VERSION@">1.0.6</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">cmv</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" />
+        </stdio>
+    </xml>
+
+    <xml name="version">
+        <version_command>
+            <![CDATA[
+                HMMV --version
+            ]]>
+        </version_command>
+    </xml>
+
+    <xml name="common_parameters">
+        <param name="alignment_filepath" type="data" format="stockholm" label="Input stockholm alignment" optional="true"/>
+        <param name="output_format" type="select" label="Output format" help="pdf, svg, png, ps">
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+            <option value="png">png</option>
+            <option value="ps">ps</option>
+        </param>
+        <param name="model_details" type="select" label="Specify visualization detail level." help="minimal,simple,detailed">
+            <option value="minimal">minimal</option>
+            <option value="simple">simple</option>
+            <option value="detailed">detailed</option>
+        </param>
+        <param name="emission_layout" type="select" label="Specify layout of emission probabilites." help="score,probability,bar">
+            <option value="score">score</option>
+            <option value="probability">probability</option>
+            <option value="bar">bar</option>
+        </param>
+        <param argument="-t" type="float" value="0.01" label="Transition probability threshold" help="Minimal value for a transition probability to be displayed (Default: 0.01)"/>
+        <param argument="-c" type="float" value="2" label="Image scaling factor" help="Set uniform scaling factor for image size (Default: 2)"/>
+        <param argument="-w" type="integer" value="100" label="Maximum image width" help="Set maximal width of result figure (Default: 100)" optional="true"/>
+        <param argument="-n" type="integer" value="50" label="Stockholm alignment entries"  help="Set cutoff for included stockholm alignment entries (Default: 50)" optional="true"/>
+    </xml>
+    
+    <xml name="vis_output">
+        <collection name="output_pdfs" type="list" label="${tool.name} on ${on_string}: output.pdfs">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.pdf" format="pdf"/>
+            <filter>common['output_format'] == 'pdf'</filter>
+        </collection>
+        <collection name="output_svg" type="list" label="${tool.name} on ${on_string}: output.svgs">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.svg" format="svg"/>
+            <filter>common['output_format'] == 'svg'</filter>
+        </collection>
+        <collection name="output_png" type="list" label="${tool.name} on ${on_string}: output.pngs">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.png" format="png"/>
+            <filter>common['output_format'] == 'png'</filter>
+        </collection>
+        <collection name="output_ps" type="list" label="${tool.name} on ${on_string}: output.ps">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.ps" format="ps"/>
+            <filter>common['output_format'] == 'ps'</filter>
+        </collection>
+    </xml>
+    
+    <token name="@COMMON_ARGS@">
+      -d $common.model_details
+      -e $common.emission_layout
+      -n $common.n
+      -w $common.w
+      -c $common.c
+      -t $common.t
+      -f $common.output_format
+      #if $common.alignment_filepath
+         -s $common.alignment_filepath
+      #end if 
+    </token>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/nar/gkt329</citation>
+        </citations>
+    </xml>
+</macros>
+