--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/meme_psp_gen.xml	Wed Aug 23 20:57:34 2017 -0400
@@ -0,0 +1,140 @@
+<tool id="meme_psp_gen" name="MEME psp-gen" version="@WRAPPER_VERSION@.0">
+    <description>- perform discriminative motif discovery</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+psp-gen
+-pos '$primary_sequence'
+-neg '$control_sequence'
+-minw $adv.minw
+-maxw $adv.maxw
+$adv.alphabet
+#if str($adv.triples_cond.triples) == 'yes':
+    -triples
+    $adv.triples_cond.fixedstart
+#end if
+$adv.equiv
+$adv.revcomp
+$adv.scalemin
+$adv.scalemax
+$adv.maxrange
+$adv.raw
+#if str($adv.report_scores_cond.report_scores) == 'yes':
+    -reportscores
+    $adv.report_scores_cond.verbose
+    2> '$output_tabular'
+#end if
+> '$output_psp'
+    ]]></command>
+    <inputs>
+        <param format="fasta" name="primary_sequence" type="data" label="Primary sequence file"/>
+        <param format="fasta" name="control_sequence" type="data" label="Control sequence file"/>
+        <section name="adv" title="Additional Options">
+            <param argument="-minw" type="integer" value="4" min="0" label="Minimum width to use for position specific priors"/>
+            <param argument="-maxw" type="integer" value="20" min="0" label="Maximum width to use for position specific priors"/>
+            <param name="alphabet" type="select" label="Alphabet">
+                <option value="-dna" selected="true">DNA</option>
+                <option value="-protein">protein</option>
+                <option value="-rna">RNA</option>
+            </param>
+            <conditional name="triples_cond">
+                <param name="triples" type="select" label="Use spaced triples instead of whole-word matches?" help="Recommended for protein">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">yes</option>
+                </param>
+                <when value="no"/>
+                <when value="yes">
+                    <param argument="-fixedstart" type="boolean" truevalue="-fixedstart" falsevalue="" checked="False" label="Allow triples to start anywhere within a site?" help="Select 'No' to only consider triples starting at the start of the site"/>
+                </when>
+            </conditional>
+            <param argument="-equiv" type="boolean" truevalue="-equiv" falsevalue="" checked="False" label="Match as equal sequences of letters that appear together?"/>
+            <param argument="-revcomp" type="boolean" truevalue="-revcomp" falsevalue="" checked="False" label="Consider both strands when calculating position specific priors for alphabets?"/>
+            <param argument="-scalemin" type="boolean" truevalue="-scalemin" falsevalue="" checked="False" label="Set the lowest score value after scaling?"/>
+            <param argument="-scalemax" type="boolean" truevalue="-scalemax" falsevalue="" checked="False" label="Set the highest score value after scaling?"/>
+            <param argument="-maxrange" type="boolean" truevalue="-maxrange" falsevalue="" checked="False" label="Choose the width with the biggest difference between minimum and maximum scores before scaling?" help="Select 'No' to choose the width with the biggest maximum score (before scaling)"/>
+            <param argument="-raw" type="boolean" truevalue="-raw" falsevalue="" checked="False" label="Output scores instead of priors?"/>
+            <conditional name="report_scores_cond">
+                <param name="report_scores" type="select" label="Output primary and control file names, scores and widths?">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">yes</option>
+                </param>
+                <when value="no"/>
+                <when value="yes">
+                    <param argument="-verbose" type="boolean" truevalue="-verbose" falsevalue="" checked="False" label="Report frequency of each score?"/>
+                </when>
+            </conditional>
+        </section>
+        <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
+            <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="memepsp" name="output_psp"/>
+        <data format="tabular" name="output_tabular" label="${tool.name} (report) on ${on_string}">
+            <filter>adv['report_scores_cond']['report_scores'] == 'yes'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="primary_sequence" value="meme_psp_protein_input.fasta" ftype="fasta"/>
+            <param name="control_sequence" value="meme_psp_protein_input.fasta" ftype="fasta"/>
+            <param name="alphabet" value="protein"/>
+            <param name="report_scores" value="yes"/>
+            <param name="verbose" value="-verbose"/>
+            <param name="non_commercial_use" value="NON_COMMERCIAL_USE"/>
+            <output name="output_psp" file="output.memepsp"/>
+            <output name="output_tabular" file="meme_psp_gen_reports_output.tabular" compare="contains"/>
+        </test>
+    </tests>
+    <help>
+
+.. class:: warningmark
+
+**WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
+Before using, be sure to review, agree, and comply with the license.**
+
+psp-gen is used to allow MEME to perform discriminative motif discovery—to find motifs overrepresented in one set of sequences compared to in another set.
+It takes two files as input—the sequence file to be input to MEME, (the "primary" file) and a "control" sequence file of sequences believed not to contain
+the same motifs as in the "primary" file. psp-gen creates a file for use by MEME that encapsulates information about probable discriminative motifs. psp-gen
+records its chosen motif width in the file, and MEME is able to adjust the data when it tries different motif widths.
+
+.. class:: infomark
+
+For detailed information on psp-gen, click here_, or view the license_.
+
+.. _here: http://meme-suite.org/doc/psp-gen.html?man_type=web
+.. _license: http://meme-suite.org/doc/copyright.html?man_type=web
+
+-----
+
+**Required options**
+
+* **Primary sequence file** - a file containing FASTA formatted sequences which are to be used as the primary set in PSP calculation.
+* **Control sequence file** - a file containing FASTA formatted sequences which are to be used as the control set in PSP calculation.
+
+**Additional options**
+
+* **Minimum width to use for position specific priors** - the minimum width to use with selecting the "best" width for PSPs.
+* **Maximum width to use for position specific priors** - the maximum width to use with selecting the "best" width for PSPs.
+* **Alphabet** - The alphabet to be used, one of DNA, protein or RNA.
+* **Use spaced triples instead of whole-word matches** - use spaced triples instead of whole-word matches (recommended when using the protein alphabet).
+
+   * **Allow triples to start anywhere within a site** - when using the -triples option, select 'Yes' to only consider triples starting at the start of the site or 'No' to allow triples to start anywhere in a width 'w' site.
+
+* **Match as equal sequences of letters that appear together** - select 'Yes' to match as equal any sequence of letter that appears together. Separate letter groups using "-" (e.g. -equiv "IVL-HKR") means treat all occurrences of I, V or L as the same, and all occurrences of H, K or R as the same.
+* **Consider both strands when calculating position specific priors for alphabets** - select 'Yes' to consider both strands when calculating PSPs for complementable alphabets or 'No to consider only the given strand.
+* **Set the lowest score value after scaling** - select 'Yes' to set the lowest score to 0.1 unless the the following "highest score" option is selected, in which case the lowest score is highest score - 1.
+* **Set the highest score value after scaling** - select 'Yes' to set the highest score to 0.9 unless the previous "lowest score" option is selected, in which case the highest score is lowest score + 1.
+* **Choose the width with the biggest difference between minimum and maximum scores before scaling** - select 'Yes' to choose the width with the biggest difference between minimum and maximum scores before scaling, or 'No' to choose the width with the biggest maximum score before scaling.
+* **Output scores instead of priors** - select 'Yes' to output scores instead of position specific priors.
+* **Output primary and control file names, scores and widths** - select 'Yes' to produce an additional tabular output consisting of control file names, lowest and highest scores and lowest and highest widths.
+
+   * **Report frequency of each score** - select 'Yes' to include the frequency of each score in the output.
+
+    </help>
+    <citations>
+        <citation type="doi">10.1186/1471-2105-11-179</citation>
+    </citations>
+</tool>