diff cmpress.xml @ 5:6e18e0b098cd draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cmpress.xml	Sat Jan 21 17:36:57 2017 -0500
@@ -0,0 +1,88 @@
+<tool id="infernal_cmpress" name="cmpress" version="@VERSION@.0">
+    <description> Prepare a covariance model database for cmscan</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+    ## CM file from the history or stored as database on disc
+    #if str($cm_opts.cm_opts_selector) == "db":
+        cmfile_path='$cm_opts.database.fields.path'
+    #else:
+        ##'$cm_opts.cmfile'
+        cmfile_path='$cmfile'
+    #end if
+    &&
+    cmpress -F "\$cmfile_path" &&
+    ##cmpress creates four files in the same directory of the cm file
+    cd `dirname "\$cmfile_path"` &&
+    tar -cvf '$outfile' `basename "\$cmfile_path"`.i1*
+]]>
+    </command>
+    <inputs>
+        <conditional name="cm_opts">
+            <param name="cm_opts_selector" type="select" label="Subject covariance models &lt;cmdb&gt; ">
+                <option value="db" >Locally installed covariance models</option>
+                <option value="histdb" selected="True">Covariance model from your history</option>
+            </param>
+            <when value="db">
+                <param name="database" type="select" label="Covariance models">
+                    <options from_file="infernal.loc">
+                        <column name="value" index="0"/>
+                        <column name="name" index="1"/>
+                        <column name="path" index="2"/>
+                    </options>
+                </param>
+            </when>
+            <when value="histdb">
+                <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
+            </when>
+        </conditional>
+
+    </inputs>
+    <outputs>
+        <data format="tar" name="outfile" label="cmpress on ${on_string}"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <conditional name="cm_opts">
+                <param name="cm_opts_selector" value="histdb"/>
+                <param name="cmfile" value="cmpress_input_minifam.cm"/>
+            </conditional>
+            <assert_stdout>
+                    <has_text text="Working...    done."/>
+            </assert_stdout>
+
+        </test>
+
+    </tests>
+    <help>
+<![CDATA[
+
+
+**What it does**
+
+Starting from a CM database <cmfile> in standard Infernal-1.1 format, construct binary compressed datafiles for cm-
+scan. The cmpress step is required for cmscan to work.
+
+**Input format**
+
+The <cmfile> must be have already been calibrated with cmcalibrate for cmpress to work.
+
+**Output format**
+
+
+
+For further questions please refere to the Infernal `Userguide <http://eddylab.org/infernal/Userguide.pdf>`_.
+
+
+]]>
+    </help>
+
+    <expand macro="citations" />
+
+
+</tool>