| Previous changeset 16:495a4173006f (2018-10-16) Next 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 e90e79e18362561d0060d2c162f1938feebdbc29 |
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modified:
macs2_callpeak.xml macs2_filterdup.xml macs2_predictd.xml macs2_randsample.xml macs2_refinepeak.xml |
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| diff -r 495a4173006f -r 424aefbd7777 macs2_callpeak.xml --- a/macs2_callpeak.xml Tue Oct 16 10:31:14 2018 -0400 +++ b/macs2_callpeak.xml Thu Apr 25 17:49:05 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.5" profile="17.09"> +<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.6" profile="17.09"> <description>Call peaks from alignment results</description> <macros> <import>macs2_macros.xml</import> @@ -138,10 +138,10 @@ <option value="Yes">Yes</option> </param> <when value="No" > - <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" label="ChIP-Seq Treatment File" /> + <param name="input_treatment_file" argument="-t" type="data" format="bam,bed" label="ChIP-Seq Treatment File" /> </when> <when value="Yes"> - <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Treatment File" /> + <param name="input_treatment_file" argument="-t" type="data" format="bam,bed" multiple="true" label="ChIP-Seq Treatment File" /> </when> </conditional> @@ -157,10 +157,10 @@ <option value="Yes">Yes</option> </param> <when value="No" > - <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" label="ChIP-Seq Control File" /> + <param name="input_control_file" argument="-c" type="data" format="bam,bed" label="ChIP-Seq Control File" /> </when> <when value="Yes"> - <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Control File" /> + <param name="input_control_file" argument="-c" type="data" format="bam,bed" multiple="true" label="ChIP-Seq Control File" /> </when> </conditional> </when> |
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| diff -r 495a4173006f -r 424aefbd7777 macs2_filterdup.xml --- a/macs2_filterdup.xml Tue Oct 16 10:31:14 2018 -0400 +++ b/macs2_filterdup.xml Thu Apr 25 17:49:05 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="macs2_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.0"> +<tool id="macs2_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.1"> <description>Remove duplicate reads at the same position</description> <macros> <import>macs2_macros.xml</import> @@ -23,7 +23,7 @@ ]]> </command> <inputs> - <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> + <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" /> <expand macro="conditional_effective_genome_size" /> <expand macro="tag_size" /> <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="Default=1e-5 (--pvalue)" /> |
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| diff -r 495a4173006f -r 424aefbd7777 macs2_predictd.xml --- a/macs2_predictd.xml Tue Oct 16 10:31:14 2018 -0400 +++ b/macs2_predictd.xml Thu Apr 25 17:49:05 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0"> +<tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.1"> <description>Predict 'd' or fragment size from alignment results</description> <macros> <import>macs2_macros.xml</import> @@ -26,7 +26,7 @@ Rscript predictd ]]></command> <inputs> - <param name="infiles" type="data" format="bam,sam,bed" multiple="True" + <param name="infiles" type="data" format="bam,bed" multiple="True" label="ChIP-seq alignment file" help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" /> <expand macro="conditional_effective_genome_size" /> |
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| diff -r 495a4173006f -r 424aefbd7777 macs2_randsample.xml --- a/macs2_randsample.xml Tue Oct 16 10:31:14 2018 -0400 +++ b/macs2_randsample.xml Thu Apr 25 17:49:05 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="macs2_randsample" name="MACS2 randsample" version="@VERSION_STRING@.0"> +<tool id="macs2_randsample" name="MACS2 randsample" version="@VERSION_STRING@.1"> <description>Randomly sample number or percentage of total reads</description> <macros> <import>macs2_macros.xml</import> @@ -24,7 +24,7 @@ #end if ]]></command> <inputs> - <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> + <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" /> <expand macro="tag_size" /> <conditional name="method_options"> <param name="method_options_selector" type="select" label="Select action to be performed"> |
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| diff -r 495a4173006f -r 424aefbd7777 macs2_refinepeak.xml --- a/macs2_refinepeak.xml Tue Oct 16 10:31:14 2018 -0400 +++ b/macs2_refinepeak.xml Thu Apr 25 17:49:05 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.0"> +<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.1"> <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description> <macros> <import>macs2_macros.xml</import> @@ -17,7 +17,7 @@ --ofile '${ outfile }' ]]></command> <inputs> - <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> + <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" /> <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" /> <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/> <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" /> |