| Previous changeset 18:640d3af5d833 (2022-04-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 7bd4238efae0d755b6a0dfff8daa43a228f18d96 |
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modified:
macs2_bdgbroadcall.xml macs2_bdgcmp.xml macs2_bdgdiff.xml macs2_bdgpeakcall.xml macs2_callpeak.xml macs2_filterdup.xml macs2_macros.xml macs2_predictd.xml macs2_randsample.xml macs2_refinepeak.xml test-data/callpeak_part.tabular |
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| diff -r 640d3af5d833 -r 86e2413cf3f8 macs2_bdgbroadcall.xml --- a/macs2_bdgbroadcall.xml Sat Apr 02 21:37:38 2022 +0000 +++ b/macs2_bdgbroadcall.xml Mon Oct 16 13:18:37 2023 +0000 |
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| @@ -1,11 +1,11 @@ <tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> - <description>Call broad peaks from bedGraph output</description> - <expand macro="bio_tools"/> + <description>Call broad peaks from bedGraph output</description> <macros> <import>macs2_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"> - <requirement type="package" version="4.1.3">gawk</requirement> + <requirement type="package" version="5.1.0">gawk</requirement> </expand> <expand macro="stdio" /> <expand macro="version_command" /> |
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| diff -r 640d3af5d833 -r 86e2413cf3f8 macs2_bdgcmp.xml --- a/macs2_bdgcmp.xml Sat Apr 02 21:37:38 2022 +0000 +++ b/macs2_bdgcmp.xml Mon Oct 16 13:18:37 2023 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="macs2_bdgcmp" name="MACS2 bdgcmp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Deduct noise by comparing two signal tracks in bedGraph</description> - <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> |
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| diff -r 640d3af5d833 -r 86e2413cf3f8 macs2_bdgdiff.xml --- a/macs2_bdgdiff.xml Sat Apr 02 21:37:38 2022 +0000 +++ b/macs2_bdgdiff.xml Mon Oct 16 13:18:37 2023 +0000 |
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| @@ -1,11 +1,11 @@ <tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Differential peak detection based on paired four bedgraph files</description> - <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"> - <requirement type="package" version="4.1.3">gawk</requirement> + <requirement type="package" version="5.1.0">gawk</requirement> </expand> <expand macro="stdio" /> <expand macro="version_command" /> |
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| diff -r 640d3af5d833 -r 86e2413cf3f8 macs2_bdgpeakcall.xml --- a/macs2_bdgpeakcall.xml Sat Apr 02 21:37:38 2022 +0000 +++ b/macs2_bdgpeakcall.xml Mon Oct 16 13:18:37 2023 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> - <description>Call peaks from bedGraph output</description> - <expand macro="bio_tools"/> + <description>Call peaks from bedGraph output</description> <macros> <import>macs2_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="stdio" /> <expand macro="version_command" /> |
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| diff -r 640d3af5d833 -r 86e2413cf3f8 macs2_callpeak.xml --- a/macs2_callpeak.xml Sat Apr 02 21:37:38 2022 +0000 +++ b/macs2_callpeak.xml Mon Oct 16 13:18:37 2023 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="macs2_callpeak" name="MACS2 callpeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> - <description>Call peaks from alignment results</description> - <expand macro="bio_tools"/> + <description>Call peaks from alignment results</description> <macros> <import>macs2_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"> </expand> <expand macro="stdio" /> @@ -218,7 +218,7 @@ </param> <section name="advanced_options" title="Advanced Options"> - <param name="to_large" argument="--to-large" type="boolean" truevalue="--to-large" falsevalue="" checked="false" + <param argument="--to-large" type="boolean" truevalue="--to-large" falsevalue="" checked="false" label="When set, scale the small sample up to the bigger sample" 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. Default: No"/> <param argument="--nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="false" @@ -244,7 +244,7 @@ help="value is either p-value or q-value as specified above (--broad-cutoff)"/> </when> <when value="nobroad"> - <param name="call_summits" argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false" + <param argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false" label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"/> </when> </conditional> @@ -313,8 +313,8 @@ <param name="outputs" value="peaks_tabular,bdg,html"/> <param name="effective_genome_size_options_selector" value="user_defined" /> <param name="gsize" value="3300000000" /> - <param name="lower" value="5" /> - <param name="upper" value="50" /> + <param name="mfold_lower" value="5" /> + <param name="mfold_upper" value="50" /> <assert_command> <has_text text="--buffer-size"/> <has_text text="--d-min"/> @@ -340,8 +340,8 @@ <param name="outputs" value="pdf"/> <param name="effective_genome_size_options_selector" value="user_defined" /> <param name="gsize" value="3300000000" /> - <param name="lower" value="5" /> - <param name="upper" value="50" /> + <param name="mfold_lower" value="5" /> + <param name="mfold_upper" value="50" /> <output name="output_plot" file="magic.pdf" compare="sim_size" ftype="pdf"/> </test> <!-- Ensure BAMPE works --> |
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| diff -r 640d3af5d833 -r 86e2413cf3f8 macs2_filterdup.xml --- a/macs2_filterdup.xml Sat Apr 02 21:37:38 2022 +0000 +++ b/macs2_filterdup.xml Mon Oct 16 13:18:37 2023 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="macs2_filterdup" name="MACS2 filterdup" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Remove duplicate reads at the same position</description> - <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> |
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| diff -r 640d3af5d833 -r 86e2413cf3f8 macs2_macros.xml --- a/macs2_macros.xml Sat Apr 02 21:37:38 2022 +0000 +++ b/macs2_macros.xml Mon Oct 16 13:18:37 2023 +0000 |
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| @@ -1,10 +1,10 @@ <macros> - <token name="@TOOL_VERSION@">2.2.7.1</token> + <token name="@TOOL_VERSION@">2.2.9.1</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">macs2</requirement> - <requirement type="package" version="3.4">r-base</requirement> + <requirement type="package" version="4.3">r-base</requirement> <yield /> </requirements> </xml> |
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| diff -r 640d3af5d833 -r 86e2413cf3f8 macs2_predictd.xml --- a/macs2_predictd.xml Sat Apr 02 21:37:38 2022 +0000 +++ b/macs2_predictd.xml Mon Oct 16 13:18:37 2023 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="macs2_predictd" name="MACS2 predictd" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Predict 'd' or fragment size from alignment results</description> - <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="stdio" /> <expand macro="version_command" /> |
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| diff -r 640d3af5d833 -r 86e2413cf3f8 macs2_randsample.xml --- a/macs2_randsample.xml Sat Apr 02 21:37:38 2022 +0000 +++ b/macs2_randsample.xml Mon Oct 16 13:18:37 2023 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="macs2_randsample" name="MACS2 randsample" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> - <description>Randomly sample number or percentage of total reads</description> + <description>Randomly sample number or percentage of total reads</description> + <macros> + <import>macs2_macros.xml</import> + </macros> <expand macro="bio_tools"/> - <macros> - <import>macs2_macros.xml</import> - </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> |
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| diff -r 640d3af5d833 -r 86e2413cf3f8 macs2_refinepeak.xml --- a/macs2_refinepeak.xml Sat Apr 02 21:37:38 2022 +0000 +++ b/macs2_refinepeak.xml Mon Oct 16 13:18:37 2023 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description> - <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> |
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| diff -r 640d3af5d833 -r 86e2413cf3f8 test-data/callpeak_part.tabular --- a/test-data/callpeak_part.tabular Sat Apr 02 21:37:38 2022 +0000 +++ b/test-data/callpeak_part.tabular Mon Oct 16 13:18:37 2023 +0000 |
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| @@ -1,4 +1,4 @@ -# This file is generated by MACS version 2.2.7.1 +# This file is generated by MACS version 2.2.9.1 # Command line: callpeak -t /tmp/tmpnaqc0336/files/3/f/0/dataset_3f02f858-205a-41bb-bfbc-712b99093ecb.dat --name ChIP_200K_bed -c /tmp/tmpnaqc0336/files/e/4/5/dataset_e45de785-43dc-44da-badd-fd49fc164b85.dat --format BED --gsize 3300000000 --keep-dup 1 --d-min 20 --buffer-size 100000 --bdg --qvalue 0.05 --mfold 5 50 --bw 300 # ARGUMENTS LIST: # name = ChIP_200K_bed |