Mercurial > repos > iuc > macs2
changeset 15:c33686854b19 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 30858afbdbe0223d07d2936a8469295bcbeda786
| author | iuc |
|---|---|
| date | Mon, 15 Oct 2018 06:49:16 -0400 |
| parents | c16dbe4e2db2 |
| children | 495a4173006f |
| files | macs2_callpeak.xml macs2_predictd.xml test-data/predictd_on_ChIP_200K_and_Control_200K.txt |
| diffstat | 3 files changed, 10 insertions(+), 19 deletions(-) [+] |
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--- a/macs2_callpeak.xml Mon Aug 06 10:41:57 2018 -0400 +++ b/macs2_callpeak.xml Mon Oct 15 06:49:16 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.4" profile="17.09"> +<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.5" profile="17.09"> <description>Call peaks from alignment results</description> <macros> <import>macs2_macros.xml</import> @@ -45,6 +45,7 @@ $advanced_options.nolambda $advanced_options.to_large + $advanced_options.spmr #if $advanced_options.ratio: --ratio $advanced_options.ratio @@ -219,6 +220,9 @@ help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. (--to-large). Default: No"/> <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" optional="True" label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming (--nolambda). Default: No"/> + <param name="spmr" type="boolean" truevalue="--SPMR" falsevalue="" checked="False" optional="True" + label="Save signal per million reads for fragment pileup profiles" + help="Requires 'Scores in bedGraph files (--bdg)' output to be selected. (--SPMR). Default: No"/> <param name="ratio" type="float" optional="True" label="When set, use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling" help="(--ratio) Default: ignore"/>
--- a/macs2_predictd.xml Mon Aug 06 10:41:57 2018 -0400 +++ b/macs2_predictd.xml Mon Oct 15 06:49:16 2018 -0400 @@ -48,7 +48,11 @@ <param name="band_width" value="300"/> <param name="lower" value="5"/> <param name="upper" value="50"/> - <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt" lines_diff="2"/> + <output name="outfile"> + <assert_contents> + <has_line line="# predicted fragment length is 284 bps" /> + </assert_contents> + </output> <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/> </test> </tests>
--- a/test-data/predictd_on_ChIP_200K_and_Control_200K.txt Mon Aug 06 10:41:57 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -# read alignment files... -# read treatment tags... -Detected format is -Detected format is -tag size is determined as 86 bps -# tag size = 86 -# total tags in alignment file -# Build Peak Model... -#2 looking for paired plus/minus strand peaks... -#2 number of paired peaks -start model_add_line... -start X-correlation... -end of X-cor -# finished! -# predicted fragment length is 284 bps -# alternative fragment length(s) may be 284 bps -# Generate R script for model