| Next changeset 1:59d58008c40d (2012-11-23) |
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Commit message:
Uploaded |
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added:
annotatePeaks.xml bed2pos.xml pos2bed.xml |
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| diff -r 000000000000 -r 2103c773690f annotatePeaks.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annotatePeaks.xml Fri Nov 09 00:53:35 2012 -0500 |
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| @@ -0,0 +1,41 @@ +<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 000000000000 -r 2103c773690f bed2pos.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bed2pos.xml Fri Nov 09 00:53:35 2012 -0500 |
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| @@ -0,0 +1,34 @@ +<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 000000000000 -r 2103c773690f pos2bed.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pos2bed.xml Fri Nov 09 00:53:35 2012 -0500 |
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| @@ -0,0 +1,34 @@ +<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> + |