| Previous changeset 0:6845ddcd5588 (2015-07-02) |
|
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan commit 608bf2d6f11fe6dceaa0060f729bdbb66cfee867 |
|
modified:
gotohscan.xml |
|
removed:
tool_dependencies.xml |
| b |
| diff -r 6845ddcd5588 -r c172fed9eb75 gotohscan.xml --- a/gotohscan.xml Thu Jul 02 12:06:30 2015 -0400 +++ b/gotohscan.xml Sun Nov 12 06:10:23 2017 -0500 |
| [ |
| @@ -3,26 +3,21 @@ <requirements> <requirement type="package" version="1.3">gotohscan</requirement> </requirements> - <stdio> - <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/> - <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error"/> - </stdio> <version_command><![CDATA[GotohScan --version | sed -n -e 2p]]></version_command> - <command><![CDATA[ - GotohScan + <command detect_errors="aggressive"><![CDATA[ +GotohScan + -d '$dbase' + -q '$query' - -d $dbase - -q $query - - #if $split and $split is not None + #if $split --split $split #end if - #if $e and $e is not None + #if $e -e $e #end if - #if $p and $p is not None + #if $p -p $p #end if @@ -31,17 +26,17 @@ > #if $o.value == '0' - $output0 + '$output0' #elif $o.value == '1' - $output1 + '$output1' #elif $o.value == '2' - $output2 + '$output2' #elif $o.value == '3' - $output3 + '$output3' #elif $o.value == '4' - $output4 + '$output4' #elif $o.value == '5' - $output5 + '$output5' #end if ]]></command> <inputs> @@ -90,12 +85,14 @@ </tests> <help> <![CDATA[ + **GotohScan** is a search tool that finds shorter sequences (usually genes) in large database sequences (chromosomes, genomes, ..) by computing all semi-global alignments. Thus, the query sequence is never truncated or split into subsequences, but always mapped to the database over its complete length. The alignment is computed via the Gotoh-alignment algorithm using affine gap costs. + ]]></help> <citations> <citation type="doi">10.1093/nar/gkn1084</citation> |
| b |
| diff -r 6845ddcd5588 -r c172fed9eb75 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jul 02 12:06:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,21 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="gotohscan" version="1.3"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/GotohScan/GotohScan-1.3.tar.gz</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>GotohScan</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - <environment_variable name="GOTOHSCAN_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme> - </readme> - </package> -</tool_dependency> |