| Next changeset 1:09955cea320f (2017-02-22) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty |
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added:
hcluster_sg.xml test-data/exam-1.txt test-data/hcluster_sg1.txt test-data/hcluster_sg2.txt tool_dependencies.xml |
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| diff -r 000000000000 -r 4a233271d05a hcluster_sg.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hcluster_sg.xml Fri Nov 11 06:56:10 2016 -0500 |
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| @@ -0,0 +1,69 @@ +<tool id="hcluster_sg" name="hcluster_sg" version="0.5.1"> + <description>Hierarchically clustering on a sparse graph</description> + <requirements> + <requirement type="package" version="0.5.1">hcluster_sg</requirement> + </requirements> + <command> +<![CDATA[ +hcluster_sg +-w $w +-s $s +-m $m +$c +-b $b +$O.O_selector +#if $O.O_selector == '-O' + -r $O.r +#end if +#if $C + -C $C +#end if +-L $L +$inputFile +> $outputFile +]]> + </command> + <inputs> + <param name="inputFile" type="data" format="tabular" label="Weight file" help="3-columns format: id-1 id-2 integer-weight" /> + <param name="w" type="integer" min="0" value="20" label="Minimum edge weight" help="(-w)" /> + <param name="s" type="float" value="0.5" label="Minimum edge density between a join" help="(-s)" /> + <param name="m" type="integer" value="500" label="Maximum size" help="(-m)" /> + <param name="c" type="boolean" truevalue="-c" falsevalue="" label="Only find single-linkage clusters" help="Bypass h-cluster (-c)" /> + <param name="b" type="float" value="0.1" label="Breaking edge density" help="(-b)" /> + <conditional name="O"> + <param name="O_selector" type="select" label="Use once-fail-inactive-forever mode" help="(-O)"> + <option value="-O">Yes</option> + <option value="" selected="true">No</option> + </param> + <when value="-O"> + <param name="r" type="integer" value="5" label="Weight resolution" help="(-r)" /> + </when> + <when value="" /> + </conditional> + <param name="C" type="data" format="tabular" optional="true" label="Category file" help="(-C)" /> + <param name="L" type="integer" value="2" label="Stringency level" help="(-L)" /> + </inputs> + <outputs> + <data format="tabular" name="outputFile" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="inputFile" ftype="tabular" value="exam-1.txt" /> + <output name="outputFile" file="hcluster_sg1.txt" /> + </test> + <test> + <param name="inputFile" ftype="tabular" value="exam-1.txt" /> + <param name="c" value="true" /> + <output name="outputFile" file="hcluster_sg2.txt" /> + </test> + </tests> + <help> +<![CDATA[ +Simple wrapper for `hcluster_sg`_. + +.. _hcluster_sg: https://github.com/douglasgscofield/hcluster +]]> + </help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r 4a233271d05a test-data/exam-1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exam-1.txt Fri Nov 11 06:56:10 2016 -0500 |
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|
| b |
| diff -r 000000000000 -r 4a233271d05a test-data/hcluster_sg1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hcluster_sg1.txt Fri Nov 11 06:56:10 2016 -0500 |
| b |
| @@ -0,0 +1,9 @@ +0 0 57 1.000 0 13 11,0,4,3,5,12,7,10,13,2,1,6,9, +1 0 23 0.671 0 46 45,39,71,83,49,61,64,38,25,72,44,29,90,35,30,28,62,65,63,88,89,34,82,73,52,74,17,55,41,56,59,51,32,33,87,31,85,27,48,66,50,37,60,77,26,54, +2 0 0 1.000 0 1 84, +3 0 33 1.000 0 8 101,96,92,98,94,100,91,99, +4 0 28 1.000 0 4 40,43,76,42, +5 0 0 1.000 0 1 8, +6 0 54 1.000 0 8 18,23,21,15,22,20,14,16, +7 0 15 0.596 0 17 24,95,58,69,78,36,68,70,57,67,97,79,53,47,75,86,46, +8 0 0 1.000 0 1 102, |
| b |
| diff -r 000000000000 -r 4a233271d05a test-data/hcluster_sg2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hcluster_sg2.txt Fri Nov 11 06:56:10 2016 -0500 |
| b |
| @@ -0,0 +1,5 @@ +0 99 0,13,39,84,83,96,101,100,99,98,76,43,8,42,40,14,24,86,97,95,102,79,78,75,70,69,68,67,58,57,53,47,46,36,23,22,21,20,18,16,15,94,92,91,90,89,88,87,85,73,41,38,33,27,26,25,17,82,77,74,72,71,66,65,64,63,62,61,60,59,56,55,54,52,51,50,49,48,45,44,34,32,31,37,35,30,29,28,12,11,10,9,7,6,5,4,3,2,1, +1 1 19, +2 1 80, +3 1 81, +4 1 93, |
| b |
| diff -r 000000000000 -r 4a233271d05a tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Nov 11 06:56:10 2016 -0500 |
| b |
| @@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="hcluster_sg" version="0.5.1"> + <install version="1.0"> + <actions> + <action type="shell_command">git clone https://github.com/douglasgscofield/hcluster.git hcluster_sg</action> + <action type="shell_command">make</action> + <action type="make_directory">$INSTALL_DIR/bin</action> + <action type="move_file"> + <source>hcluster_sg</source> + <destination>$INSTALL_DIR/bin/</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +hcluster_sg is tool for hierarchically clustering on a sparse graph. + </readme> + </package> +</tool_dependency> |