--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minced.xml	Mon May 05 04:23:26 2014 -0400
@@ -0,0 +1,119 @@
+<tool id="crispr_recognition_tool" name="detect CRISPR sequences" version="0.1.5">
+    <description>(minced)</description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="50" merge_outputs="output,output_region,output_ggf_full,output_ggf,output_fasta" />
+    <requirements>
+        <requirement type="package" version="0.1.5">minced</requirement>
+        <requirement type="set_environment">MINCED_SCRIPT_PATH</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range=":-1" level="fatal" />
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+    <command>
+        temp_output=\$(mktemp);
+        minced
+            -minNR $minNR
+            -minRL $minRL
+            -maxRL $maxRL
+            -minSL $minSL
+            -maxSL $maxSL
+            #if str($searchWL) != 'none':
+                -searchWL $searchWL
+            #end if
+            $input
+            \$temp_output
+            #if '-spacers' in str($outputs).split():
+                -spacers
+            #end if 
+            #if '-gffFull' in str($outputs).split():
+                -gffFull
+            #end if
+            #if '-gff' in str($outputs).split():
+                -gff
+            #end if
+            ;
+
+            python \$MINCED_SCRIPT_PATH/reformat.py \$temp_output results.bed results.tab;
+            #if '-spacers' in str($outputs).split():
+                mv \$temp_output'_spacers.fa' $output_fasta;
+            #end if
+    </command>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/>
+
+        <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have"/>
+        <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region"/>
+        <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region"/>
+        <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region"/>
+        <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region"/>
+        <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs">
+            <option value="none" selected="true">default</option>
+            <option value="6">6</option>
+            <option value="7">7</option>
+            <option value="8">8</option>
+            <option value="9">9</option>
+        </param>
+
+        <param name="outputs" type="select" multiple="True" label="Additional output format" help="Please select a output format.">
+            <option value="-gff">summary results in gff format</option>
+            <option value="BED" selected="true">summary results in BED format</option>
+            <option value="-gffFull">detailed results in gff format</option>
+            <option value="TABULAR" selected="true">detailed results in tabular format</option>
+            <option value="-spacers">fasta formatted file containing the spacers</option>
+            <validator type="no_options" message="Please select at least one output file." />
+        </param>
+
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" from_work_dir="results.tab" label="${tool.name} on ${on_string}">
+            <filter>'TABULAR' in outputs</filter>
+        </data>
+        <data format="bed" name="output_region" from_work_dir="results.bed" label="${tool.name} on ${on_string} - BED file">
+            <filter>'BED' in outputs</filter>
+        </data>
+        <data format="gff3" name="output_ggf_full" from_work_dir="results_full.gff" label="${tool.name} on ${on_string} - GFF file extended">
+            <filter>'-gffFull' in outputs</filter>
+        </data>
+        <data format="gff3" name="output_gff" from_work_dir="results.gff" label="${tool.name} on ${on_string} - GFF file">
+            <filter>'-gff' in outputs</filter>
+        </data>
+        <data format="fasta" name="output_fasta" label="${tool.name} on ${on_string} - GFF file">
+            <filter>'-spacers' in outputs</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="sequence.fasta" ftype="fasta" />
+            <param name="minNR" value="3" />
+            <param name="minRL" value="29" />
+            <param name="maxRL" value="38" />
+            <param name="minSL" value="19" />
+            <param name="maxSL" value="48" />
+            <param name="searchWL" value="none" />
+            <output name="output" file="minced.tabular" ftype="tabular" />
+            <output name="output_region" file="minced.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+MinCED - Mining CRISPRs in Environmental Datasets
+
+
+MinCED is a program to find Clustered Regularly Interspaced Short Palindromic
+Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes,
+in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the
+command-line and was derived from CRT (http://www.room220.com/crt/).
+
+https://github.com/ctSkennerton/minced
+
+**Citation**
+
+For the underlying tool, please cite `Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P:
+CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007 Jun 18;8(1):209`
+
+If you use this tool in Galaxy, please cite Gruening, BA et al. https://github.com/bgruening/galaxytools
+
+    </help>
+</tool>
+