| Previous changeset 35:be178f712bb1 (2014-06-29) Next changeset 37:3ce2cf776363 (2014-06-30) |
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Commit message:
Refactor normalize-by-median; use a virtualenv to install khmer |
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modified:
normalize-by-median.xml tool_dependencies.xml |
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| diff -r be178f712bb1 -r 846232fc30bf normalize-by-median.xml --- a/normalize-by-median.xml Sun Jun 29 18:13:23 2014 -0400 +++ b/normalize-by-median.xml Mon Jun 30 12:04:43 2014 -0400 |
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| @@ -21,13 +21,12 @@ --ksize=20 --n_tables=4 --min-tablesize=$parameters.tablesize - --cutoff=20 #else --ksize=$parameters.ksize --n_tables=$parameters.n_tables --min-tablesize=$parameters.tablesize_specific - --cutoff=$parameters.cutoff #end if + --cutoff=$cutoff #if $save_countingtable --savetable=$countingtable #end if @@ -60,12 +59,16 @@ type="boolean" label="Save the k-mer counting table(s) in a file" help="" /> - + <param name="cutoff" + type="integer" + min="1" + value="20" + label="cutoff" /> <conditional name="parameters"> <param name="type" type="select" label="Advanced Parameters" - help="ksize, n_tabless, a specific tablesize, cutoff" > + help="ksize, n_tables, a specific tablesize" > <option value="simple" selected="true"> Hide @@ -110,11 +113,6 @@ type="text" label="tablesize" help="lower bound on the tablesize to use" /> - <param name="cutoff" - type="integer" - min="1" - value="20" - label="cutoff" /> </when> </conditional> </inputs> @@ -134,9 +132,12 @@ <tests> <test interactor="api"> - <param name="inputs" value="test-abund-read-2.fa"/> - <param name="cutoff" value="1" /> - <param name="ksize" value="17" /> + <conditional name="parameters"> + <param name="type" value="specific" /> + <param name="inputs" value="test-abund-read-2.fa"/> + <param name="cutoff" value="1" /> + <param name="ksize" value="17" /> + </conditional> <output name="output"> <discover_dataset name="test-abund-read-2.fa.keep"> <assert_contents> |
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| diff -r be178f712bb1 -r 846232fc30bf tool_dependencies.xml --- a/tool_dependencies.xml Sun Jun 29 18:13:23 2014 -0400 +++ b/tool_dependencies.xml Mon Jun 30 12:04:43 2014 -0400 |
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| @@ -3,7 +3,7 @@ <package name="khmer" version="1.1"> <install version="1.0"> <actions> - <action type="shell_command">easy_install -U setuptools==3.4.1; pip install --user khmer==1.1 || pip install khmer==1.1</action> + <action type="setup_virtualenv">setuptools==3.4.1 khmer==1.1</action> </actions> </install> </package> |