changeset 4:08e4ca411ea6 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty

Binary file minced.tar.bz2 has changed

--- a/minced.xml	Mon May 05 04:29:36 2014 -0400
+++ b/minced.xml	Sun Sep 18 06:18:17 2016 -0400
@@ -1,15 +1,15 @@
-<tool id="minced" name="detect CRISPR sequences" version="0.1.5">
+<tool id="minced" name="detect CRISPR sequences" version="0.2.0">
     <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" />
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="250" 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>
+        <requirement type="package" version="0.2.0">minced</requirement>
     </requirements>
     <stdio>
         <exit_code range=":-1" level="fatal" />
         <exit_code range="1:" level="fatal" />
     </stdio>
     <command>
+<![CDATA[
         temp_output=\$(mktemp);
         minced
             -minNR $minNR
@@ -24,7 +24,7 @@
             \$temp_output
             #if '-spacers' in str($outputs).split():
                 -spacers
-            #end if 
+            #end if
             #if '-gffFull' in str($outputs).split():
                 -gffFull
             #end if
@@ -33,10 +33,11 @@
             #end if
             ;
 
-            python \$MINCED_SCRIPT_PATH/reformat.py \$temp_output results.bed results.tab;
+            python $__tool_directory__/reformat.py \$temp_output results.bed results.tab;
             #if '-spacers' in str($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"/>
@@ -95,6 +96,7 @@
         </test>
     </tests>
     <help>
+<![CDATA[
 **What it does**
 
 MinCED - Mining CRISPRs in Environmental Datasets
@@ -107,13 +109,13 @@
 
 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>
+    <citations>
+        <citation type="doi">10.1186/1471-2105-8-209 </citation>
+    </citations>
 </tool>
 

--- a/tool_dependencies.xml	Mon May 05 04:29:36 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="MINCED_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-    <package name="minced" version="0.1.5">
-        <repository changeset_revision="d6bd09fb54da" name="package_minced_0_1_5" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>