diff crt.xml @ 0:ad026c2db3e9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/crt.xml	Fri May 02 06:14:11 2014 -0400
@@ -0,0 +1,74 @@
+<tool id="crispr_recognition_tool" name="CRISPR Recognition Tool" version="1.2.0">
+    <description>(CRT)</description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="1" merge_outputs="output,output_region" />
+    <requirements>
+        <requirement type="package" version="1.2">crisper_recognition_tool</requirement>
+        <requirement type="set_environment">CRISPR_RECOGNITION_TOOL_SCRIPT_PATH</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range=":-1" level="fatal" />
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+    <command>
+        temp_output=\$(mktemp);
+        java -cp \$CRISPR_RECOGNITION_TOOL_JAR_PATH/CRT1.2-CLI.jar crt
+            -minNR $minNR
+            -minRL $minRL
+            -maxRL $maxRL
+            -minSL $minSL
+            -maxSL $maxSL
+            #if str($searchWL) != 'none':
+                -searchWL $searchWL
+            #end if
+            $input
+            \$temp_output
+            ;
+
+            python \$CRISPR_RECOGNITION_TOOL_SCRIPT_PATH/reformat.py \$temp_output $output_region $output
+    </command>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/>
+
+        <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have"/>
+        <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region"/>
+        <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region"/>
+        <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region"/>
+        <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region"/>
+        <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs">
+            <option value="none" selected="true">default</option>
+            <option value="6">6</option>
+            <option value="7">7</option>
+            <option value="8">8</option>
+            <option value="9">9</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
+        <data format="bed" name="output_region" label="${tool.name} on ${on_string} - BED file" />
+    </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="crt.tabular" ftype="tabular" />
+            <output name="output_region" file="crt.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help>
+CRISPR Recognition Tool - a tool for automatic detection of clustered regularly interspaced palindromic repeats
+
+http://www.room220.com/crt/
+
+**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`
+
+    </help>
+</tool>
+