| Next changeset 1:0ffee257645e (2018-05-16) |
|
Commit message:
planemo upload commit 8c3aff54626caa56e8396ef25308754ef4beb3c5 |
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added:
README.rst test-data/amaVit1_Gallus/amaVit1_Gallus.pos.psl test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_filtered_valid.psl test-data/dbia3/dbia3_dmel.pos.psl test-data/dbia3/dbia3_dmel_filtered_valid.psl tool_dependencies.xml ucsc_pslpostarget.xml |
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| diff -r 000000000000 -r fe51c5a974b5 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Apr 12 17:51:28 2017 -0400 |
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| @@ -0,0 +1,20 @@ +Galaxy wrapper for UCSC pslPosTarget tool (version: v340) +========================================================== + +flip psl strands so target is positive and implicit + +usage: +------- + + $ pslPosTarget inPsl outPsl + +options: + +Source code: +------------- + +http://hgdownload.cse.ucsc.edu/admin/exe/ + +Licence +------- +Please note that commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics (http://www.kentinformatics.com). |
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| diff -r 000000000000 -r fe51c5a974b5 test-data/amaVit1_Gallus/amaVit1_Gallus.pos.psl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amaVit1_Gallus/amaVit1_Gallus.pos.psl Wed Apr 12 17:51:28 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +1247 370 0 44 6 280 17 96639 - NM_001012804 4592 121 2062 LMAW01000001.1 10443977 517465 615765 18 139,137,107,81,142,58,94,3,171,39,114,150,87,2,112,74,32,119, 2530,2669,2806,2914,2995,3137,3195,3289,3292,3487,3721,3844,4036,4123,4125,4246,4320,4352, 517465,522996,528389,528742,532090,534170,535128,538977,539062,544916,550155,550655,561249,562375,562390,574639,615514,615646, +420 114 0 0 4 99 3 7093 + NM_001031013 971 69 702 LMAW01000002.1 5883884 3610886 3618513 5 33,66,21,276,138, 69,138,232,285,564, 3610886,3610955,3617941,3618099,3618375, +3724 1107 0 326 14 609 44 22663 + NM_204766 5992 49 5815 LMAW01000002.1 5883884 103604 131424 45 51,78,132,3,152,2,29,75,90,63,1,95,81,3,136,119,150,2,169,180,123,48,90,117,123,134,241,261,177,146,90,72,267,129,81,2,196,348,116,193,106,123,177,99,87, 49,154,256,388,391,543,545,574,691,781,844,845,967,1048,1051,1187,1306,1456,1458,1627,1807,1960,2008,2098,2215,2338,2472,2713,2974,3151,3298,3388,3493,3778,3943,4024,4026,4222,4696,4812,5051,5212,5335,5608,5728, 103604,104407,107764,107909,108002,108233,108257,109261,112047,112967,113036,113148,114257,114391,114866,116183,116438,116593,116908,117767,118030,118682,120119,120672,121329,122185,122724,123518,123945,124449,124904,125793,125898,126790,127405,127543,127717,128055,129238,129442,129761,130020,130254,131103,131337, |
| b |
| diff -r 000000000000 -r fe51c5a974b5 test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_filtered_valid.psl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_filtered_valid.psl Wed Apr 12 17:51:28 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +1247 370 0 44 6 280 17 96639 +- NM_001012804 4592 121 2062 LMAW01000001.1 10443977 517465 615765 18 119,32,74,112,2,87,150,114,39,171,3,94,58,142,81,107,137,139, 121,240,272,355,467,469,598,757,1066,1129,1300,1303,1397,1455,1597,1679,1786,1923, 9828212,9828431,9869264,9881475,9881600,9882641,9893172,9893708,9899022,9904744,9904997,9908755,9909749,9911745,9915154,9915481,9920844,9926373, +420 114 0 0 4 99 3 7093 ++ NM_001031013 971 69 702 LMAW01000002.1 5883884 3610886 3618513 5 33,66,21,276,138, 69,138,232,285,564, 3610886,3610955,3617941,3618099,3618375, +3724 1107 0 326 14 609 44 22663 ++ NM_204766 5992 49 5815 LMAW01000002.1 5883884 103604 131424 45 51,78,132,3,152,2,29,75,90,63,1,95,81,3,136,119,150,2,169,180,123,48,90,117,123,134,241,261,177,146,90,72,267,129,81,2,196,348,116,193,106,123,177,99,87, 49,154,256,388,391,543,545,574,691,781,844,845,967,1048,1051,1187,1306,1456,1458,1627,1807,1960,2008,2098,2215,2338,2472,2713,2974,3151,3298,3388,3493,3778,3943,4024,4026,4222,4696,4812,5051,5212,5335,5608,5728, 103604,104407,107764,107909,108002,108233,108257,109261,112047,112967,113036,113148,114257,114391,114866,116183,116438,116593,116908,117767,118030,118682,120119,120672,121329,122185,122724,123518,123945,124449,124904,125793,125898,126790,127405,127543,127717,128055,129238,129442,129761,130020,130254,131103,131337, |
| b |
| diff -r 000000000000 -r fe51c5a974b5 test-data/dbia3/dbia3_dmel.pos.psl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dbia3/dbia3_dmel.pos.psl Wed Apr 12 17:51:28 2017 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r fe51c5a974b5 test-data/dbia3/dbia3_dmel_filtered_valid.psl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dbia3/dbia3_dmel_filtered_valid.psl Wed Apr 12 17:51:28 2017 -0400 |
| b |
| b'@@ -0,0 +1,651 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|
| b |
| diff -r 000000000000 -r fe51c5a974b5 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Apr 12 17:51:28 2017 -0400 |
| b |
| @@ -0,0 +1,23 @@ +<?xml version="1.0"?> +<tool_dependency> + <!-- required tools: + -pslPosTarget + --> + <package name="ucsc_tools_340_for_BLAT" version="1.0"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/package_ucsc_tools_340_for_BLAT.tar.gz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + </actions> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions_group> + </install> + <readme>The tools and utilities were created by the UCSC Genome Bioinformatics Group</readme> + </package> +</tool_dependency> \ No newline at end of file |
| b |
| diff -r 000000000000 -r fe51c5a974b5 ucsc_pslpostarget.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsc_pslpostarget.xml Wed Apr 12 17:51:28 2017 -0400 |
| [ |
| @@ -0,0 +1,65 @@ +<?xml version="1.0"?> +<tool id="ucsc_pslpostarget" name="UCSC pslPosTarget" version="1.0"> + <description>flip psl strands so target is positive and implicit</description> + <requirements> + <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="warning" description="invalid entries" /> + </stdio> + <command><![CDATA[ + pslPosTarget + '${input_psl}' + '${output_psl}' +]]></command> + <inputs> + <param type="data" name="input_psl" format="psl" /> + </inputs> + <outputs> + <data format="psl" name="output_psl" label="${tool.name} on ${on_string}"></data> + </outputs> + <tests> + <test> + <param name="input_psl" value="amaVit1_Gallus/amaVit1_Gallus_gallus_filtered_valid.psl" /> + <output name="output_psl" value="amaVit1_Gallus/amaVit1_Gallus.pos.psl" /> + </test> + <test> + <param name="input_psl" value="dbia3/dbia3_dmel_filtered_valid.psl" /> + <output name="output_psl" value="dbia3/dbia3_dmel.pos.psl" /> + </test> + + </tests> + <help> + <![CDATA[ +pslPosTarget +============= + +- flip psl strands so target is positive and implicit + +usage: + + pslPosTarget inPsl outPsl + +Source code (v340): +++++++++++++++++++++ + +userApps.v340.src.tgz: http://hgdownload.cse.ucsc.edu/admin/exe/ + +]]></help> +<citations> + <citation type="bibtex">@article{kent2002blat, + title={BLAT—the BLAST-like alignment tool}, + author={Kent, W James}, + journal={Genome research}, + volume={12}, + number={4}, + pages={656--664}, + year={2002}, + publisher={Cold Spring Harbor Lab} + }</citation> +</citations> +</tool> + + + + |