| Previous changeset 0:c5a812cdf478 (2016-12-09) Next changeset 2:27e62af48a5a (2016-12-11) |
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Commit message:
planemo upload |
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modified:
countmatrixforedger.xml plotheatmap.xml |
| b |
| diff -r c5a812cdf478 -r ddde82ae5dea countmatrixforedger.xml --- a/countmatrixforedger.xml Fri Dec 09 10:52:35 2016 -0500 +++ b/countmatrixforedger.xml Sun Dec 11 18:57:58 2016 -0500 |
| [ |
| @@ -9,7 +9,6 @@ echo -e ${s.sample_data}"\t"${s.sample_name}"\t"${s.sample_group} >> script.data; #end for# - cat script.data > /tmp/script.data; $__tool_directory__/tools/scrsh.sh script.data; cat count.matrix > $count_matrix; @@ -27,29 +26,12 @@ </repeat> </inputs> <outputs> -<!-- <data name="output" format="data" /> --> <data name="count_matrix" format="data" /> <data name="annotation" format="data" /> <data name="log" format="data" /> <data name="error_log" format="data" /> </outputs> <tests> -<!-- <test> - <param name="sample_0|sample_data" value="data1" /> - <param name="sample_1|sample_data" value="data2" /> - <param name="sample_2|sample_data" value="data3" /> - <param name="sample_3|sample_data" value="data4" /> - <param name="sample_0|sample_name" value="sample1" /> - <param name="sample_1|sample_name" value="sample2" /> - <param name="sample_2|sample_name" value="sample3" /> - <param name="sample_3|sample_name" value="sample4" /> - <param name="sample_0|sample_group" value="gr1" /> - <param name="sample_1|sample_group" value="gr1" /> - <param name="sample_2|sample_group" value="gr2" /> - <param name="sample_3|sample_group" value="gr2" /> - <output name="output" file="output"/> - - </test> --> <test> <param name="sample_0|sample_data" value="data1" /> <param name="sample_1|sample_data" value="data2" /> @@ -72,24 +54,10 @@ </tests> <help> <![CDATA[ - -tutaj cos bedzie ]]> </help> <citations> - <citation type="bibtex"> - @article{Berenger2014, - doi = {10.1186/1758-2946-6-23}, - url = {http://dx.doi.org/10.1186/1758-2946-6-23}, - year = {2014}, - publisher = {Springer Nature}, - volume = {6}, - number = {1}, - pages = {23}, - author = {Francois Berenger and Arnout Voet and Xiao Lee and Kam YJ Zhang}, - title = {A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening}, - journal = {Journal of Cheminformatics} - } + <citation> </citation> </citations> </tool> |
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| diff -r c5a812cdf478 -r ddde82ae5dea plotheatmap.xml --- a/plotheatmap.xml Fri Dec 09 10:52:35 2016 -0500 +++ b/plotheatmap.xml Sun Dec 11 18:57:58 2016 -0500 |
| [ |
| @@ -1,5 +1,5 @@ -<tool id="plotheatmap" name="plotheatmap" version="1.0"> - <description>Make a count matrix for edgeR</description> +<tool id="plotheatmap" name="plotHeatmap" version="1.0"> + <description>Plot heatmap</description> <stdio> <exit_code range="1:" /> </stdio> @@ -7,8 +7,6 @@ <![CDATA[ $__tool_directory__/tools/script.R $count_matrix $stats_matrix $log_fc $log_cpm $pvalue $fdr > $rscript_log 2> $rerror_log - - ]]> </command> <inputs> @@ -21,7 +19,6 @@ </inputs> <outputs> -<!-- <data name="output" format="data" /> --> <data format="pdf" name="haetamappdf" from_work_dir="heatmap.pdf" > <filter>(outftype == 'pdf')</filter> </data> @@ -37,7 +34,6 @@ <param name="log_cpm" value="2"/> <param name="pvalue" value="0.05"/> <param name="fdr" value="0.1"/> -<!-- <output name="output" file="done"/> --> <output name="haetamappdf" file="heatmap.pdf" ftype="pdf" compare="sim_size" /> <output name="rscript_log" file="rscript.log"/> <output name="rerror_log" file="rerror.log"/> @@ -47,11 +43,8 @@ </tests> <help> <![CDATA[ - -tutaj cos bedzie ]]> </help> <citations> - </citations> </tool> \ No newline at end of file |