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changeset 1:43b1f073b693 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
author bgruening
date Tue, 30 Jun 2015 16:23:23 -0400
parents 5314e5d6f040
children 616efa22d193
files cat.xml easyjoin.xml grep.xml readme.rst sort.xml test-data/cat_result1.txt text_processing.tar.bz2 tool_dependencies.xml
diffstat 8 files changed, 182 insertions(+), 45 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cat.xml	Tue Jun 30 16:23:23 2015 -0400
@@ -0,0 +1,74 @@
+<tool id="tp_cat" name="Concatenate datasets" version="0.1.0">
+    <description>tail-to-head (cat)</description>
+    <requirements>
+        <requirement type="package" version="8.22">gnu_coreutils</requirement>
+    </requirements>
+    <version_command>
+    <![CDATA[
+        cat --version | head -n 1
+    ]]>
+    </version_command>
+    <command>
+    <![CDATA[
+        cat
+            #for $file in $inputs:
+                "${file}"
+            #end for
+        > $out_file1
+    ]]></command>
+    <inputs>
+        <param name="inputs" multiple="true" type="data" format="txt" label="datasets to concatenate"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format_source="inputs" metadata_source="inputs"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" value="sort_result1.bed,sort_result2.bed,sort_result3.bed"/>
+            <output name="out_file1" file="cat_result1.txt"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: warningmark
+
+**WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This tool does not check if the datasets being concatenated are in the same format.
+
+-----
+
+**What it does**
+
+Concatenates datasets
+
+-----
+
+**Example**
+
+Concatenating Dataset::
+
+    chrX  151087187  151087355  A  0  -
+    chrX  151572400  151572481  B  0  +
+
+with Dataset1::
+
+    chr1  151242630  151242955  X  0  +
+    chr1  151271715  151271999  Y  0  +
+    chr1  151278832  151279227  Z  0  -
+
+and with Dataset2::
+
+    chr2  100000030  200000955  P  0  +
+    chr2  100000015  200000999  Q  0  +
+
+will result in the following::
+
+    chrX  151087187  151087355  A  0  -
+    chrX  151572400  151572481  B  0  +
+    chr1  151242630  151242955  X  0  +
+    chr1  151271715  151271999  Y  0  +
+    chr1  151278832  151279227  Z  0  -
+    chr2  100000030  200000955  P  0  +
+    chr2  100000015  200000999  Q  0  +
+]]></help>
+</tool>
--- a/easyjoin.xml	Thu Jan 29 07:53:17 2015 -0500
+++ b/easyjoin.xml	Tue Jun 30 16:23:23 2015 -0400
@@ -3,15 +3,13 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="set_environment">TP_SCRIPT_PATH</requirement>
-    </expand>
+    <expand macro="requirements" />
     <version_command>join --version | head -n 1</version_command>
     <command>
 <![CDATA[
-        cp \$TP_SCRIPT_PATH/sort-header ./ &&
+        cp $__tool_directory__/sort-header ./ &&
         chmod +x sort-header &&
-        perl \$TP_SCRIPT_PATH/easyjoin
+        perl $__tool_directory__/easyjoin
             $jointype
             -t '	'
             $header
--- a/grep.xml	Thu Jan 29 07:53:17 2015 -0500
+++ b/grep.xml	Tue Jun 30 16:23:23 2015 -0400
@@ -5,7 +5,6 @@
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="2.14">gnu_grep</requirement>
-        <requirement type="set_environment">TP_SCRIPT_PATH</requirement>
     </expand>
     <version_command>grep --version | head -n 1</version_command>
     <command>
@@ -20,7 +19,7 @@
                 $invert
                 $case_sensitive
                 -- "${url_paste}"
-                '${infile}' | \$TP_SCRIPT_PATH/ansi2html.sh > "${output}"
+                '${infile}' | $__tool_directory__/ansi2html.sh > "${output}"
         #else:
             grep
                 -P
--- a/readme.rst	Thu Jan 29 07:53:17 2015 -0500
+++ b/readme.rst	Tue Jun 30 16:23:23 2015 -0400
@@ -1,8 +1,8 @@
 Galaxy wrappers for common unix text-processing tools
 =====================================================
 
-The initial work was done by Assaf Gordon and Greg Hannon's lab ( http://hannonlab.cshl.edu ) 
-in Cold Spring Harbor Laboratory ( http://www.cshl.edu ). In late 2013 maintainence and 
+The initial work was done by Assaf Gordon and Greg Hannon's lab ( http://hannonlab.cshl.edu )
+in Cold Spring Harbor Laboratory ( http://www.cshl.edu ). In late 2013 maintainence and
 further development was taken over by Bjoern Gruening. Feel free to contribute any general purpose
 text manipulation tool to this repository.
 
@@ -58,19 +58,19 @@
 
 User trying to run an awk program similar to::
 
- BEGIN { system("ls") }
+  BEGIN { system("ls") }
 
 Will get an error (in Galaxy) saying::
 
- fatal: 'system' function not allowed in sandbox mode.
+  fatal: 'system' function not allowed in sandbox mode.
 
 User trying to run a SED program similar to::
 
- 1els
+  1els
 
 will get an error (in Galaxy) saying::
 
- sed: -e expression #1, char 2: e/r/w commands disabled in sandbox mode
+  sed: -e expression #1, char 2: e/r/w commands disabled in sandbox mode
 
 That being said, if you do find some vulnerability in these tools, please let me know and I'll try fix them.
 
@@ -103,22 +103,21 @@
   * Copyright (c) 2013-2015   B. Gruening  (bjoern dot gruening <at> gmail dot com)
 
 
-Permission is hereby granted, free of charge, to any person obtaining 
-a copy of this software and associated documentation files (the 
-"Software"), to deal in the Software without restriction, including 
-without limitation the rights to use, copy, modify, merge, publish, 
-distribute, sublicense, and/or sell copies of the Software, and to 
-permit persons to whom the Software is furnished to do so, subject to 
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
 the following conditions:
 
-The above copyright notice and this permission notice shall be 
+The above copyright notice and this permission notice shall be
 included in all copies or substantial portions of the Software.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 
-IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY 
-CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 
-TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 
-SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 
-
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
--- a/sort.xml	Thu Jan 29 07:53:17 2015 -0500
+++ b/sort.xml	Tue Jun 30 16:23:23 2015 -0400
@@ -77,7 +77,7 @@
             <repeat name="sortkeys">
                 <param name="column" value="1"/>
                 <param name="style" value=""/>
-            <param name="order" value=""/>
+                <param name="order" value=""/>
             </repeat>
             <repeat name="sortkeys">
                 <param name="column" value="3"/>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cat_result1.txt	Tue Jun 30 16:23:23 2015 -0400
@@ -0,0 +1,70 @@
+# comment 1 \n\n''" again
+# comment 2 **}"''' special
+# comment 3 @n/n""" characters
+chr1	148185113	148187485	NM_002796	0	+	148185136	148187378	0	7	163,207,147,82,117,89,120,	0,416,877,1199,1674,1977,2252,
+chr1	148077485	148111797	NM_002651	0	-	148078400	148111728	0	12	1097,121,133,266,124,105,110,228,228,45,937,77,	0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235,
+chr1	147984101	148035079	BC007833	0	+	147984545	148033414	0	14	529,32,81,131,118,153,300,206,84,49,85,130,46,1668,	0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310,
+chr1	147962006	147975713	NM_005997	0	-	147962192	147975670	0	6	574,145,177,115,153,160,	0,1543,7859,9048,9340,13547,
+chr2	220229182	220233943	NM_024536	0	-	220229609	220233765	0	4	1687,180,574,492,	0,1990,2660,4269,
+chr2	220108603	220116964	NM_001927	0	+	220108689	220116217	0	9	664,61,96,162,126,221,44,83,789,	0,1718,1874,2118,2451,2963,5400,7286,7572,
+chr2	118389378	118390700	BC005078	0	-	118390395	118390500	0	1	1322,	0,
+chr2	118288484	118306183	NM_006773	0	+	118288583	118304530	0	14	184,285,144,136,101,200,115,140,162,153,114,57,178,1796,	0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903,
+chr5	131621285	131637046	NM_003687	0	+	131621326	131635821	0	7	134,152,82,179,164,118,1430,	0,4915,8770,13221,13609,14097,14331,
+chr5	131556201	131590458	NM_004199	0	-	131556601	131582218	0	15	471,97,69,66,54,100,71,177,194,240,138,152,97,100,170,	0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087,
+chr5	131424245	131426795	NM_000588	0	+	131424298	131426383	0	5	215,42,90,42,535,	0,313,1658,1872,2015,
+chr5	131170738	131357870	AF099740	0	-	131311206	131357817	0	31	112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248,	0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884,
+chr6	108722790	108950942	NM_145315	0	+	108722976	108950321	0	13	325,224,52,102,131,100,59,83,71,101,141,114,750,	0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402,
+chr6	108639410	108689143	NM_152827	0	-	108640045	108688818	0	3	741,125,487,	0,2984,49246,
+chr6	108593954	108616704	NM_003269	0	+	108594662	108615360	0	9	733,146,88,236,147,97,150,106,1507,	0,5400,8778,10445,12037,14265,14749,15488,21243,
+chr6	108298214	108386086	NM_007214	0	-	108299600	108385906	0	21	1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304,	0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568,
+chr7	116944658	117107512	AF377960	0	-	116945541	116979926	0	23	1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173,	0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681,
+chr7	116713967	116902666	NM_000492	0	+	116714099	116901113	0	27	185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754,	0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945,
+chr7	116511232	116557294	NM_003391	0	-	116512159	116556994	0	5	1157,265,278,227,383,	0,20384,37843,43339,45679,
+chr7	113320332	113924911	AK131266	0	+	113862563	113893433	0	20	285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124,	0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455,
+chr8	118880786	119193239	NM_000127	0	-	118881131	119192466	0	11	531,172,161,90,96,119,133,120,108,94,1735,	0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718,
+chr9	128849867	128870133	NM_020145	0	-	128850516	128869987	0	11	757,241,101,90,24,63,93,134,129,142,209,	0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057,
+chr9	128789530	128848928	NM_015354	0	+	128789552	128848511	0	44	54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594,	0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804,
+chr9	128787362	128789566	NM_014908	0	-	128787519	128789136	0	1	2204,	0,
+chr9	128763240	128783870	NM_174933	0	+	128764156	128783586	0	12	261,118,74,159,76,48,56,63,129,117,127,370,	0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260,
+chrX	152693677	152712545	NM_001666	0	-	152694029	152712503	0	22	586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109,	0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759,
+chrX	152691216	152693487	NM_000054	0	+	152691446	152693029	0	3	255,885,664,	0,616,1607,
+chrX	152648233	152662158	NM_000425	0	-	152648964	152662138	0	28	963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100,	0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825,
+chrX	122719582	122773357	NM_001167	0	+	122745047	122766566	0	7	96,909,100,79,43,201,6985,	0,25433,28421,31040,32533,40295,46790,
+# comment 1 \n\n''" again
+# comment 2 **}"''' special
+# comment 3 @n/n""" characters
+chr1	147962006	147975713	NM_005997	0	-	147962192	147975670	0	6	574,145,177,115,153,160,	0,1543,7859,9048,9340,13547,
+chr1	147984101	148035079	BC007833	0	+	147984545	148033414	0	14	529,32,81,131,118,153,300,206,84,49,85,130,46,1668,	0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310,
+chr1	148077485	148111797	NM_002651	0	-	148078400	148111728	0	12	1097,121,133,266,124,105,110,228,228,45,937,77,	0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235,
+chr1	148185113	148187485	NM_002796	0	+	148185136	148187378	0	7	163,207,147,82,117,89,120,	0,416,877,1199,1674,1977,2252,
+chr2	118288484	118306183	NM_006773	0	+	118288583	118304530	0	14	184,285,144,136,101,200,115,140,162,153,114,57,178,1796,	0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903,
+chr2	118389378	118390700	BC005078	0	-	118390395	118390500	0	1	1322,	0,
+chr2	220108603	220116964	NM_001927	0	+	220108689	220116217	0	9	664,61,96,162,126,221,44,83,789,	0,1718,1874,2118,2451,2963,5400,7286,7572,
+chr2	220229182	220233943	NM_024536	0	-	220229609	220233765	0	4	1687,180,574,492,	0,1990,2660,4269,
+chr5	131170738	131357870	AF099740	0	-	131311206	131357817	0	31	112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248,	0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884,
+chr5	131424245	131426795	NM_000588	0	+	131424298	131426383	0	5	215,42,90,42,535,	0,313,1658,1872,2015,
+chr5	131556201	131590458	NM_004199	0	-	131556601	131582218	0	15	471,97,69,66,54,100,71,177,194,240,138,152,97,100,170,	0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087,
+chr5	131621285	131637046	NM_003687	0	+	131621326	131635821	0	7	134,152,82,179,164,118,1430,	0,4915,8770,13221,13609,14097,14331,
+chr6	108298214	108386086	NM_007214	0	-	108299600	108385906	0	21	1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304,	0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568,
+chr6	108593954	108616704	NM_003269	0	+	108594662	108615360	0	9	733,146,88,236,147,97,150,106,1507,	0,5400,8778,10445,12037,14265,14749,15488,21243,
+chr6	108639410	108689143	NM_152827	0	-	108640045	108688818	0	3	741,125,487,	0,2984,49246,
+chr6	108722790	108950942	NM_145315	0	+	108722976	108950321	0	13	325,224,52,102,131,100,59,83,71,101,141,114,750,	0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402,
+chr7	113320332	113924911	AK131266	0	+	113862563	113893433	0	20	285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124,	0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455,
+chr7	116511232	116557294	NM_003391	0	-	116512159	116556994	0	5	1157,265,278,227,383,	0,20384,37843,43339,45679,
+chr7	116713967	116902666	NM_000492	0	+	116714099	116901113	0	27	185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754,	0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945,
+chr7	116944658	117107512	AF377960	0	-	116945541	116979926	0	23	1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173,	0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681,
+chr8	118880786	119193239	NM_000127	0	-	118881131	119192466	0	11	531,172,161,90,96,119,133,120,108,94,1735,	0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718,
+chr9	128763240	128783870	NM_174933	0	+	128764156	128783586	0	12	261,118,74,159,76,48,56,63,129,117,127,370,	0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260,
+chr9	128787362	128789566	NM_014908	0	-	128787519	128789136	0	1	2204,	0,
+chr9	128789530	128848928	NM_015354	0	+	128789552	128848511	0	44	54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594,	0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804,
+chr9	128849867	128870133	NM_020145	0	-	128850516	128869987	0	11	757,241,101,90,24,63,93,134,129,142,209,	0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057,
+chrX	122719582	122773357	NM_001167	0	+	122745047	122766566	0	7	96,909,100,79,43,201,6985,	0,25433,28421,31040,32533,40295,46790,
+chrX	152648233	152662158	NM_000425	0	-	152648964	152662138	0	28	963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100,	0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825,
+chrX	152691216	152693487	NM_000054	0	+	152691446	152693029	0	3	255,885,664,	0,616,1607,
+chrX	152693677	152712545	NM_001666	0	-	152694029	152712503	0	22	586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109,	0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759,
+chr1	300	400	feature4	1.1e-05	+
+chr20	800	900	feature2	1.1	+
+chr10	100	200	feature1	100.01	+
+chr21	300	500	feature5	1.1e2	+
+chr2	500	600	feature3	1000.1	+
+chr15	700	800	feature6	1.1e4	+
Binary file text_processing.tar.bz2 has changed
--- a/tool_dependencies.xml	Thu Jan 29 07:53:17 2015 -0500
+++ b/tool_dependencies.xml	Tue Jun 30 16:23:23 2015 -0400
@@ -1,32 +1,29 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="gnu_coreutils" version="8.22">
-      <repository changeset_revision="ac64dfe4b1fb" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="gnu_coreutils" version="8.22">
+        <repository changeset_revision="ac64dfe4b1fb" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="gnu_awk" version="4.1.0">
-      <repository changeset_revision="52a8268bb49f" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="52a8268bb49f" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="gnu_grep" version="2.14">
-      <repository changeset_revision="42bbeb602ba9" name="package_gnu_grep_2_14" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="42bbeb602ba9" name="package_gnu_grep_2_14" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="gnu_sed" version="4.2.2-sandbox">
-      <repository changeset_revision="76cc52f79dd4" name="package_gnu_sed_4_2_2_sandbox" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="76cc52f79dd4" name="package_gnu_sed_4_2_2_sandbox" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <set_environment version="1.0">
-      <environment_variable action="set_to" name="TP_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
     <package name="perl" version="5.18.1">
-      <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="text_processing_perl_packages" version="1.0">
-      <install version="1.0">
-          <actions>
-              <action type="setup_perl_environment">
-                  <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                      <package name="perl" version="5.18.1" />
+        <install version="1.0">
+            <actions>
+                <action type="setup_perl_environment">
+                    <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="perl" version="5.18.1" />
                     </repository>
-                    <!-- allow downloading and installing an Perl package from cpan.org-->
-                    <package>https://cpan.metacpan.org/authors/id/S/SA/SALVA/Sort-Key-1.33.tar.gz</package>
+                   <!-- allow downloading and installing an Perl package from cpan.org-->
+                   <package>https://cpan.metacpan.org/authors/id/S/SA/SALVA/Sort-Key-1.33.tar.gz</package>
                 </action>
             </actions>
         </install>