diff cmstat.xml @ 5:6e18e0b098cd draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86

--- a/cmstat.xml	Mon Dec 19 15:27:06 2016 -0500
+++ b/cmstat.xml	Sat Jan 21 17:36:57 2017 -0500
@@ -1,30 +1,25 @@
-<tool id="infernal_cmstat" name="Summary statistics" version="1.1.0.1">
-    <description>for covariance model (cmstat)</description>
-    <requirements>
-        <requirement type="package">infernal</requirement>
-        <requirement type="package" version="1.1">infernal</requirement>
-        <requirement type="package" version="8.22">gnu_coreutils</requirement>
-    </requirements>
+<tool id="infernal_cmstat" name="cmstat" version="@VERSION@.0">
+    <description>Summary statistics for covariance model </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio" />
     <command>
 <![CDATA[
         ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
         ## it will be converted to a tab delimited file and piped to Galaxy
-        temp_tabular_output=\$(mktemp);
+        ##temp_tabular_output=\$(mktemp);
 
         cmstat
-
             #if str($cm_opts.cm_opts_selector) == "db":
                 $cm_opts.database.fields.path
             #else:
                 $cm_opts.cmfile
             #end if
 
-            > \$temp_tabular_output
-            ;
+            > $outfile
 
-            ## 1. replace all lines starting # (comment lines)
-            ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
-            sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile
 
 ]]>
     </command>
@@ -51,6 +46,21 @@
     <outputs>
         <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
     </outputs>
+    <tests>
+        <test>
+            <conditional name="cm_opts">
+                <param name="cm_opts_selector" value="histdb"/>
+                <param name="cmfile" value="cmstat_input.cm"/>
+            </conditional>
+            <output name="outfile" >
+                <assert_contents>
+                    <has_text text="idx"/>
+                    <has_text text="accession"/>
+                    <has_text text="nseq"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help>
 <![CDATA[
 
@@ -86,21 +96,10 @@
      relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs.
 
 
-For further questions please refere to the Infernal `Userguide <http://selab.janelia.org/software/infernal/Userguide.pdf>`_.
+For further questions please refere to the Infernal `Userguide <http://eddylab.org/infernal/Userguide.pdf>`_.
 
 ]]>
     </help>
-    <citations>
-        <citation type="doi">10.1093/bioinformatics/btt509</citation>
-        <citation type="bibtex">
-            @ARTICLE{bgruening_galaxytools,
-                Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
-                keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
-                title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
-                url = {https://github.com/bgruening/galaxytools}
-            }
-        </citation>
-    </citations>
-  
-    
+    <expand macro="citations" />
+
 </tool>