--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/micomplete.xml	Thu Oct 17 08:39:52 2013 -0400
@@ -0,0 +1,90 @@
+<tool id="micomplete" name="micomplete" version="0.1">
+  <description>Using hmm profiles of conserved proteins, reports how much complete a (single-cell amplified) genome is</description>
+  <requirements>
+    <requirement type="package" version="3.1b1">hmmer</requirement>
+  </requirements>
+  <command interpreter="perl">micomplete.pl 
+  #if $hmm_source.hmm_source_type == "cached"
+  --hmm "${ hmm_source.profiles.fields.hmms }"
+  --weights "${ hmm_source.profiles.fields.weights }"
+  #else
+  --hmm "${ hmm_source.own_profiles }"
+    #if $hmm_source.weights.use_weights
+    --weights "${ hmm_source.weights.own_weights }"
+    #end if
+  #end if
+  --proteome $proteome
+  --cut-off $cutoff
+  #if $evalue
+  --evalue 
+  #end if
+  #if $save_hmm_tab
+  --save-hmm-tab $hmm_tab
+  #end if
+  #if $save_hmm_alignments
+  --save-hmm-alignments $hmm_alignments
+  #end if
+  #if $save_res_tab
+  --save-result-tab $res_tab
+  #end if
+  --threads $threads > $output
+  </command>
+  <inputs>
+    <param name="proteome" type="data" format="fasta" label="Proteome file" />
+    <conditional name="hmm_source">
+      <param name="hmm_source_type" type="select" label="HMM file from history or from built-in profile?">
+	<option value="cached">Use a built-in profile</option>
+	<option value="history">Use a profile from the history</option>
+      </param>
+      <when value="cached">
+	<param name="profiles" type="select" label="Select a reference set">
+	  <options from_data_table="micomplete_hmms">
+	    <filter type="sort_by" column="2" />
+	  </options>
+	</param>
+      </when>
+      <when value="history">
+	<param name="own_profiles" type="data" format="text" label="Select a HMM set in the history" />
+	<conditional name="weights">
+	  <param name="use_weights" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Use weights?" />
+	  <when value="True">
+	    <param name="own_weights" type="data" format="tabular" label="Select a weight file (optional)" help="There should be exactly one weight for each profile in the profiles file"/>
+	  </when>
+	</conditional>
+      </when>
+    </conditional>
+    <param name="cutoff" type="float" value="1e-10" label="E-value cutoff to include hits" />
+    <param name="evalue" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Show E-values on the output instead of 0/1?" />
+    <param name="save_res_tab" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Save per marker result tabular file?" />
+    <param name="save_hmm_tab" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Save HMM tab result file?" />
+    <param name="save_hmm_alignments" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Save HMM alignments result file?" />
+    <param name="threads" type="integer" value="15" min="1" label="Number of threads to use" />
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" label="Completeness report" />
+    <data format="tabular" name="res_tab" label="HMM report, tabular format"> 
+      <filter>save_res_tab is True</filter>
+    </data>
+    <data format="tabular" name="hmm_tab" label="HMM report, tabular format"> 
+      <filter>save_hmm_tab is True</filter>
+    </data>
+    <data format="txt" name="hmm_alignments" label="HMM alignments"> 
+      <filter>save_hmm_alignments is True</filter>
+    </data>
+  </outputs>
+  <help>
+***What it does***
+
+Micomplete estimates the level of completion of a genome. This is particularly useful for single-cell amplified genomes. It aligns a proteome to a set of "markers" or conserved proteins, represented by a collection of HMM profiles, possibly with weights. It uses hmmsearch (http://hmmer.janelia.org/, see for example S.R Eddy, PLOS Comp Biol 2011, 7:e1002195) to align proteins
+
+Weights are used to alleviate the effect of having/not having a specific contig which would contain many markers that are generally clustering together. Typically, ribosomal proteins, often used are markers, are often organized in operons. Thus, the impact of having/not having these operons is very important, and should be downplayed to get a more correct estimate.
+
+**License**
+
+This wrapper is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.
+  </help>
+</tool>
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