| Previous changeset 0:2103c773690f (2012-11-09) Next changeset 2:7268cbc535e5 (2012-11-23) |
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Commit message:
Deleted selected files |
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removed:
annotatePeaks.xml bed2pos.xml pos2bed.xml |
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| diff -r 2103c773690f -r 59d58008c40d annotatePeaks.xml --- a/annotatePeaks.xml Fri Nov 09 00:53:35 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,41 +0,0 @@ -<tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.2"> - <requirements> - <requirement type="package">homer</requirement> - </requirements> - <description></description> - <!--<version_command></version_command>--> - <command> - annotatePeaks.pl $input_bed $genome_selector 1> $out_annotated - 2> $out_log || echo "Error running annotatePeaks." >&2 - </command> - <inputs> - <param format="tabular,bed" name="input_bed" type="data" label="Homer peak positions or BED format" /> - <param name="genome_selector" type="select" label="Genome version"> - <option value="hg19" selected="true">hg19</option> - </param> - </inputs> - <outputs> - <!--<data format="html" name="html_outfile" label="index" />--> - <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> - <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" /> - <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.log" /> - </outputs> - <tests> - <test> - <!--<param name="input_file" value="extract_genomic_dna.fa" />--> - <!--<output name="html_file" file="sample_output.html" ftype="html" />--> - </test> - </tests> - - <help> - - .. class:: infomark - - **Homer annoatePeaks** - More information on accepted formats - http://biowhat.ucsd.edu/homer/ngs/annotation.html - - - </help> -</tool> - |
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| diff -r 2103c773690f -r 59d58008c40d bed2pos.xml --- a/bed2pos.xml Fri Nov 09 00:53:35 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,34 +0,0 @@ -<tool id="homer_bed2pos" name="homer_bed2pos" version="0.0.2"> - <requirements> - <requirement type="package">homer</requirement> - </requirements> - <description></description> - <!--<version_command></version_command>--> - <command> - bed2pos.pl $input_bed 1> $out_pos - 2> $out_log || echo "Error running bed2pos." >&2 - </command> - <inputs> - <param format="tabular,bed" name="input_bed" type="data" label="BED file" /> - </inputs> - <outputs> - <!--<data format="html" name="html_outfile" label="index" />--> - <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> - <data format="tabular" name="out_pos" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#" /> - <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#.log" /> - </outputs> - <tests> - <test> - <!--<param name="input_file" value="extract_genomic_dna.fa" />--> - <!--<output name="html_file" file="sample_output.html" ftype="html" />--> - </test> - </tests> - - <help> - .. class:: infomark - - **Homer bed2pos.pl** - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - </help> -</tool> - |
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| diff -r 2103c773690f -r 59d58008c40d pos2bed.xml --- a/pos2bed.xml Fri Nov 09 00:53:35 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,34 +0,0 @@ -<tool id="homer_pos2bed" name="homer_pos2bed" version="0.0.2"> - <requirements> - <requirement type="package">homer</requirement> - </requirements> - <description></description> - <!--<version_command></version_command>--> - <command> - pos2bed.pl $input_peak 1> $out_bed - 2> $out_log || echo "Error running pos2bed." >&2 - </command> - <inputs> - <param format="tabular" name="input_peak" type="data" label="Homer peak positions" /> - </inputs> - <outputs> - <!--<data format="html" name="html_outfile" label="index" />--> - <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> - <data format="bed" name="out_bed" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.bed" /> - <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.log" /> - </outputs> - <tests> - <test> - <!--<param name="input_file" value="extract_genomic_dna.fa" />--> - <!--<output name="html_file" file="sample_output.html" ftype="html" />--> - </test> - </tests> - - <help> - .. class:: infomark - - **Homer pos2bed.pl** - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - </help> -</tool> - |