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changeset 1:d4fb020c19ca draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation commit f3cda75b01f512edd8723f157db104fca819ce0c
author bgruening
date Tue, 13 Dec 2016 03:02:52 -0500
parents 2064ae2602b1
children
files readme.rst test-data/1.bed test-data/uniq_results1.bed test-data/uniq_results2.bed uniq.xml
diffstat 5 files changed, 314 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Tue Dec 13 03:02:52 2016 -0500
@@ -0,0 +1,48 @@
+===================================================
+Galaxy wrappers for various file manipulation tools
+===================================================
+
+This wrapper is copyright 2013 by Björn Grüning.
+
+
+============
+Installation
+============
+
+You can install the wrappers from the Galaxy `Tool Shed`_::
+
+    http://toolshed.g2.bx.psu.edu/view/bgruening/unique
+
+
+.. _`Tool Shed`: http://toolshed.g2.bx.psu.edu/
+
+=======
+History
+=======
+
+- v0.1: Initial public release
+- the uniq.xml and the sort_rows tools are moved to the unix tools
+
+
+===============================
+Wrapper Licence (MIT/BSD style)
+===============================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.bed	Tue Dec 13 03:02:52 2016 -0500
@@ -0,0 +1,128 @@
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+++ b/test-data/uniq_results1.bed	Tue Dec 13 03:02:52 2016 -0500
@@ -0,0 +1,65 @@
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+chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_r	0	-
+chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-
+chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_f	0	+
+chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+
+chr9	128787519	128789136	CCDS6915.1_cds_0_0_chr9_128787520_r	0	-
+chr9	128882427	128882523	CCDS6917.1_cds_0_0_chr9_128882428_f	0	+
+chr9	128937229	128937445	CCDS6919.1_cds_0_0_chr9_128937230_r	0	-
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+
+chr5	131556601	131556672	CCDS4151.1_cds_0_0_chr5_131556602_r	0	-
+chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+
+chr5	131847541	131847666	CCDS4155.1_cds_0_0_chr5_131847542_r	0	-
+chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-
+chr1	147984545	147984630	CCDS990.1_cds_0_0_chr1_147984546_f	0	+
+chr1	148078400	148078582	CCDS993.1_cds_0_0_chr1_148078401_r	0	-
+chr1	148185136	148185276	CCDS996.1_cds_0_0_chr1_148185137_f	0	+
+chrX	152648964	152649196	CCDS14733.1_cds_0_0_chrX_152648965_r	0	-
+chrX	152691446	152691471	CCDS14735.1_cds_0_0_chrX_152691447_f	0	+
+chrX	152694029	152694263	CCDS14736.1_cds_0_0_chrX_152694030_r	0	-
+chr2	220190202	220190242	CCDS2441.1_cds_0_0_chr2_220190203_f	0	+
+chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/uniq_results2.bed	Tue Dec 13 03:02:52 2016 -0500
@@ -0,0 +1,20 @@
+chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-
+chr10	55251623	55253124	CCDS7248.1_cds_0_0_chr10_55251624_r	0	-
+chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-
+chr12	38440094	38440321	CCDS8736.1_cds_0_0_chr12_38440095_r	0	-
+chr13	112381694	112381953	CCDS9526.1_cds_0_0_chr13_112381695_f	0	+
+chr14	98710240	98712285	CCDS9949.1_cds_0_0_chr14_98710241_r	0	-
+chr15	41486872	41487060	CCDS10096.1_cds_0_0_chr15_41486873_r	0	-
+chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+
+chr18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-
+chr19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+
+chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+
+chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-
+chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+
+chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+
+chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-
+chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+
+chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-
+chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+
+chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_f	0	+
--- a/uniq.xml	Thu May 15 12:42:00 2014 -0400
+++ b/uniq.xml	Tue Dec 13 03:02:52 2016 -0500
@@ -1,20 +1,25 @@
-<tool id="bg_uniq" name="Unique" version="0.3">
-  <description>occurrences of each record</description>
-  <command interpreter='python'>
-    uniq.py 
-        $ignore_case 
+<tool id="bg_uniq" name="unique" version="0.4">
+    <description>occurrences of each record</description>
+    <requirements>
+        <requirement type="package" version="2.7.12">python</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+    python '$__tool_directory__/uniq.py'
+        $ignore_case
         $is_numeric
         #if $adv_opts.adv_opts_selector=="advanced":
             $adv_opts.column_start
             $adv_opts.column_end
         #end if
-        $outfile
-        $input
+        '$outfile'
+        '$input'
+]]>
   </command>
   <inputs>
-    <param name="input" type="data" format="tabular,text" label="from query" /> 
-    <param name="ignore_case" type="boolean" label="ignore differences in case when comparing" truevalue="-f" falsevalue="false" checked="false" help="ignore differences in case when comparing"/>
-    <param name="is_numeric" type="boolean" label="column only contains numeric values" truevalue="-n" falsevalue="false" checked="false" help="did the calumn have numeric values"/>
+    <param name="input" type="data" format="tabular,text" label="from query" />
+    <param name="ignore_case" type="boolean" label="Ignore differences in case when comparing" truevalue="-f" falsevalue="false" checked="false" />
+    <param name="is_numeric" type="boolean" label="Column only contains numeric values" truevalue="-n" falsevalue="false" checked="false" />
     <conditional name="adv_opts">
         <param name="adv_opts_selector" type="select" label="Advanced Options">
           <option value="basic" selected="True">Hide Advanced Options</option>
@@ -32,28 +37,44 @@
   </outputs>
   <tests>
     <test>
+      <param name="input" value="1.bed"/>
+      <param name="is_numeric" value="True"/>
+      <param name="ignore_case" value="True"/>
+      <param name="adv_opts_selector" value="advanced"/>
+      <param name="column_start" value="2"/>
+      <param name="column_end" value="3"/>
+      <output name="outfile" file="uniq_results1.bed"/>
+    </test>
+    <test>
+      <param name="input" value="1.bed"/>
+      <param name="is_numeric" value="False"/>
+      <param name="ignore_case" value="True"/>
+      <param name="adv_opts_selector" value="advanced"/>
+      <param name="column_start" value="1"/>
+      <param name="column_end" value="1"/>
+      <output name="outfile" file="uniq_results2.bed"/>
     </test>
   </tests>
   <help>
-  
- .. class:: infomark
+<![CDATA[
 
-**Syntax**
+
+**What it does**
 
 This tool returns all unique lines using the 'sort -u' command.
-
------
-
-.. class:: infomark
+    
+**Input**
 
 The input file needs to be tab separated. Please convert your file if necessary.
 
------
+**Output**
 
-**Example**
+This tool returns all unique lines:
+
+Example:
 
 - Input file::
-     
+
        chr1   10  100  gene1
        chr1  105  200  gene2
        chr1   10  100  gene1
@@ -71,5 +92,16 @@
        chr3   15 1656  gene6
 
 
-</help>
+]]>
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @ARTICLE{bgruening_galaxytools,
+                Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
+                keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
+                title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
+                url = {https://github.com/bgruening/galaxytools}
+            }
+        </citation>
+    </citations>
 </tool>