Mercurial > repos > dave > all_tests_pass

changeset 1:91bd6dfe97f7

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dave
date Tue, 04 Jun 2013 09:53:52 -0400
parents c0683a002f70
children dd2ca1892880 68e581bd3a36
files changeCase.pl changeCase.xml dependency_configs/tool_dependencies.xml test-data/1.bed test-data/1.txt test-data/changeCase_out1.tabular test-data/changeCase_out2.tabular
diffstat 7 files changed, 14 insertions(+), 285 deletions(-) [+]
line wrap: on
line diff
--- a/changeCase.pl	Mon May 20 11:55:42 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-#! /usr/bin/perl -w
-
-use strict;
-use warnings;
-
-my $columns = {};
-my $del = "";
-my @in = ();
-my @out = ();
-my $command = "";
-my $field = 0;
-
-# a wrapper for changing the case of columns from within galaxy
-# isaChangeCase.pl [filename] [columns] [delim] [casing] [output]
-
-die "Check arguments: $0 [filename] [columns] [delim] [casing] [output]\n" unless @ARGV == 5;
-
-# process column input
-$ARGV[1] =~ s/\s+//g;
-foreach ( split /,/, $ARGV[1] ) {
-  if (m/^c\d{1,}$/i) {
-    s/c//ig;
-    $columns->{$_} = --$_;
-  }
-}
-
-die "No columns specified, columns are not preceeded with 'c', or commas are not used to separate column numbers: $ARGV[1]\n" if keys %$columns == 0;
-
-my $column_delimiters_href = {
-	'TAB' => q{\t},
-	'COMMA' => ",",
-	'DASH' => "-",
-	'UNDERSCORE' => "_",
-	'PIPE' => q{\|},
-	'DOT' => q{\.},
-	'SPACE' => q{\s+}
-};
-	
-$del = $column_delimiters_href->{$ARGV[2]};
-
-open (OUT, ">$ARGV[4]") or die "Cannot create $ARGV[4]:$!\n";
-open (IN,  "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n";
-while (<IN>) {
-  chop;
-  @in = split /$del/; 
-  for ( my $i = 0; $i <= $#in; ++$i) {
-	if (exists $columns->{$i}) {
-		push(@out, $ARGV[3] eq 'up' ? uc($in[$i]) : lc($in[$i]));
-	} else {
-		push(@out, $in[$i]);
-	}
-  }
-  print OUT join("\t",@out), "\n";
-  @out = ();
-}
-close IN;
-
-close OUT;
--- a/changeCase.xml	Mon May 20 11:55:42 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,77 +0,0 @@
-<tool id="ChangeCase" name="Change Case">
-  <description> of selected columns</description>
-  <stdio>
-    <exit_code range="1:" err_level="fatal" />
-  </stdio>
-  <command interpreter="perl">changeCase.pl $input "$cols" $delimiter $casing $out_file1</command>
-  <inputs>
-    <param name="input" format="txt" type="data" label="From"/>
-    <param name="cols" size="10" type="text" value="c1,c2" label="Change case of columns"/>
-    <param name="delimiter" type="select" label="Delimited by">
-      <option value="TAB">Tab</option>
-      <option value="SPACE">Whitespace</option>
-      <option value="DOT">Dot</option>
-      <option value="COMMA">Comma</option>
-      <option value="DASH">Dash</option>
-      <option value="UNDERSCORE">Underscore</option>
-      <option value="PIPE">Pipe</option>
-    </param>
-    <param name="casing" type="select" label="To">
-      <option value="up">Upper case</option>
-      <option value="lo">Lower case</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" value="1.txt" ftype="txt"/>
-      <param name="cols" value="c1"/>
-      <param name="delimiter" value="SPACE"/>
-      <param name="casing" value="up"/>
-      <output name="out_file1" file="changeCase_out1.tabular"/>
-    </test>
-    <test>
-      <param name="input" value="1.bed" ftype="bed"/>
-      <param name="cols" value="c1"/>
-      <param name="delimiter" value="TAB"/>
-      <param name="casing" value="up"/>
-      <output name="out_file1" file="changeCase_out2.tabular"/>
-    </test>
-  </tests>
-  <help>
-
-.. class:: warningmark
-
-**This tool breaks column assignments.** To re-establish column assignments run the tool and click on the pencil icon in the resulting history item.
-
-.. class:: warningmark
-
-The format of the resulting dataset from this tool is always tabular.
-
------
-
-**What it does**
-
-This tool selects specified columns from a dataset and converts the values of those columns to upper or lower case.
-
-- Columns are specified as **c1**, **c2**, and so on.
-- Columns can be specified in any order (e.g., **c2,c1,c6**)
-
------
-
-**Example**
-
-Changing columns 1 and 3 ( delimited by Comma ) to upper case in::
-
-  apple,is,good
-  windows,is,bad
-
-will result in::
-
-  APPLE is GOOD
-  WINDOWS is BAD
-
-  </help>
-</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dependency_configs/tool_dependencies.xml	Tue Jun 04 09:53:52 2013 -0400
@@ -0,0 +1,14 @@
+<tool_dependency>
+    <package name="R" version="2.15.0">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_r_2_15" owner="boris" changeset_revision="0eb8a25c2c00" />
+    </package>
+    <package name="ape" version="3.0-8">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_ape_3_0" owner="boris" changeset_revision="8dafccd90485" />
+    </package>
+    <package name="rpy2" version="2.2.6">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_rpy2_2_2" owner="boris" changeset_revision="acd114013251" />
+    </package>
+    <package name="dendropy" version="3.12.0">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_dendropy_3_12" owner="boris" changeset_revision="304c2b5f037a" />
+    </package>
+</tool_dependency>
--- a/test-data/1.bed	Mon May 20 11:55:42 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-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	+
-chr10	55251623	55253124	CCDS7248.1_cds_0_0_chr10_55251624_r	0	-
-chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-
-chr11	116206508	116206563	CCDS8377.1_cds_0_0_chr11_116206509_f	0	+
-chr11	116211733	116212337	CCDS8378.1_cds_0_0_chr11_116211734_r	0	-
-chr11	1812377	1812407	CCDS7726.1_cds_0_0_chr11_1812378_f	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	-
-chr15	41673708	41673857	CCDS10097.1_cds_0_0_chr15_41673709_f	0	+
-chr15	41679161	41679250	CCDS10098.1_cds_0_0_chr15_41679162_r	0	-
-chr15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+
-chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+
-chr16	179963	180135	CCDS10401.1_cds_0_0_chr16_179964_r	0	-
-chr16	244413	244681	CCDS10402.1_cds_0_0_chr16_244414_f	0	+
-chr16	259268	259383	CCDS10403.1_cds_0_0_chr16_259269_r	0	-
-chr18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-
-chr18	59406881	59407046	CCDS11985.1_cds_0_0_chr18_59406882_f	0	+
-chr18	59455932	59456337	CCDS11986.1_cds_0_0_chr18_59455933_r	0	-
-chr18	59600586	59600754	CCDS11988.1_cds_0_0_chr18_59600587_f	0	+
-chr19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+
-chr19	59236026	59236146	CCDS12872.1_cds_0_0_chr19_59236027_r	0	-
-chr19	59297998	59298008	CCDS12877.1_cds_0_0_chr19_59297999_f	0	+
-chr19	59302168	59302288	CCDS12878.1_cds_0_0_chr19_59302169_r	0	-
-chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+
-chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_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	-
-chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-
-chr20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+
-chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-
-chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+
-chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+
-chr21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-
-chr21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+
-chr21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-
-chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+
-chr22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-
-chr22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+
-chr22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_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	-
-chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-
-chr6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+
-chr6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-
-chr6	108722976	108723115	CCDS5067.1_cds_0_0_chr6_108722977_f	0	+
-chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+
-chr7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-
-chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+
-chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	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	+
-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	-
-chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_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	-
--- a/test-data/1.txt	Mon May 20 11:55:42 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-chr1    4225    19670
-chr10   6       8
-chr1    24417   24420
-chr6_hla_hap2   0       150
-chr2    1       5
-chr10   2       10
-chr1    30      55
-chrY    1       20
-chr1    1225979 42287290
-chr10   7       8
--- a/test-data/changeCase_out1.tabular	Mon May 20 11:55:42 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-CHR1	4225	19670
-CHR10	6	8
-CHR1	24417	24420
-CHR6_HLA_HAP2	0	150
-CHR2	1	5
-CHR10	2	10
-CHR1	30	55
-CHRY	1	20
-CHR1	1225979	42287290
-CHR10	7	8
--- a/test-data/changeCase_out2.tabular	Mon May 20 11:55:42 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-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	+
-CHR10	55251623	55253124	CCDS7248.1_cds_0_0_chr10_55251624_r	0	-
-CHR11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-
-CHR11	116206508	116206563	CCDS8377.1_cds_0_0_chr11_116206509_f	0	+
-CHR11	116211733	116212337	CCDS8378.1_cds_0_0_chr11_116211734_r	0	-
-CHR11	1812377	1812407	CCDS7726.1_cds_0_0_chr11_1812378_f	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	-
-CHR15	41673708	41673857	CCDS10097.1_cds_0_0_chr15_41673709_f	0	+
-CHR15	41679161	41679250	CCDS10098.1_cds_0_0_chr15_41679162_r	0	-
-CHR15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+
-CHR16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+
-CHR16	179963	180135	CCDS10401.1_cds_0_0_chr16_179964_r	0	-
-CHR16	244413	244681	CCDS10402.1_cds_0_0_chr16_244414_f	0	+
-CHR16	259268	259383	CCDS10403.1_cds_0_0_chr16_259269_r	0	-
-CHR18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-
-CHR18	59406881	59407046	CCDS11985.1_cds_0_0_chr18_59406882_f	0	+
-CHR18	59455932	59456337	CCDS11986.1_cds_0_0_chr18_59455933_r	0	-
-CHR18	59600586	59600754	CCDS11988.1_cds_0_0_chr18_59600587_f	0	+
-CHR19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+
-CHR19	59236026	59236146	CCDS12872.1_cds_0_0_chr19_59236027_r	0	-
-CHR19	59297998	59298008	CCDS12877.1_cds_0_0_chr19_59297999_f	0	+
-CHR19	59302168	59302288	CCDS12878.1_cds_0_0_chr19_59302169_r	0	-
-CHR2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+
-CHR2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_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	-
-CHR20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-
-CHR20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+
-CHR20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-
-CHR20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+
-CHR21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+
-CHR21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-
-CHR21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+
-CHR21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-
-CHR22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+
-CHR22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-
-CHR22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+
-CHR22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_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	-
-CHR6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-
-CHR6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+
-CHR6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-
-CHR6	108722976	108723115	CCDS5067.1_cds_0_0_chr6_108722977_f	0	+
-CHR7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+
-CHR7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-
-CHR7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+
-CHR7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	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	+
-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	-
-CHRX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_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	-