Mercurial > repos > bgruening > crispr_recognition_tool

changeset 2:484771826337 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/crt commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55
author bgruening
date Tue, 13 Jun 2017 08:24:45 -0400
parents 2a2c0f4d2625
children 26f5abc235c2
files crt.xml tool_dependencies.xml
diffstat 2 files changed, 21 insertions(+), 40 deletions(-) [+]
line wrap: on
line diff
--- a/crt.xml	Sat May 03 05:58:17 2014 -0400
+++ b/crt.xml	Tue Jun 13 08:24:45 2017 -0400
@@ -4,15 +4,15 @@
     <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>
+<![CDATA[
         temp_output=\$(mktemp);
-        java -cp \$CRISPR_RECOGNITION_TOOL_JAR_PATH/CRT1.2-CLI.jar crt
+        crt crt
             -minNR $minNR
             -minRL $minRL
             -maxRL $maxRL
@@ -25,17 +25,18 @@
             \$temp_output
             ;
 
-            python \$CRISPR_RECOGNITION_TOOL_SCRIPT_PATH/reformat.py \$temp_output $output_region $output
+            python $__tool_directory__/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">
+        <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have" help="-minNR, default 3"/>
+        <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region" help="-minRL, default 19"/>
+        <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region" help="-maxRL, default 38"/>
+        <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region, -minSL, default 19"/>
+        <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region, -maxSL, default 48"/>
+        <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs" help="-searchWL">
             <option value="none" selected="true">default</option>
             <option value="6">6</option>
             <option value="7">7</option>
@@ -61,15 +62,20 @@
         </test>
     </tests>
     <help>
-CRISPR Recognition Tool - a tool for automatic detection of clustered regularly interspaced palindromic repeats
+<![CDATA[
+
+**What it does**
 
-http://www.room220.com/crt/
+`CRISPR Recognition Tool <http://www.room220.com/crt/>`_ is a tool for automatic detection of clustered regularly interspaced palindromic repeats (CRISPR). It rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes. 
+
+**Input**
 
-**Citation**
+DNA sequence in FASTA format
 
-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>
+    <citations>
+        <citation type="doi">10.1186/1471-2105-8-209</citation>
+    </citations>
 </tool>
 
--- a/tool_dependencies.xml	Sat May 03 05:58:17 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="CRISPR_RECOGNITION_TOOL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-    <package name="crisper_recognition_tool" version="1.2">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://www.room220.com/crt/CRT1.2-CLI.jar.zip</action>
-                <action type="move_directory_files">
-                    <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="CRISPR_RECOGNITION_TOOL_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
-</tool_dependency>
-
-
-