Mercurial > repos > rnateam > metilene
diff metilene.xml @ 6:f9883968b113 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit 090bc9bb5c775600f4727d8729a032b52e78bd05-dirty
| author | rnateam |
|---|---|
| date | Thu, 17 Dec 2015 17:09:39 -0500 |
| parents | b6263bd3666f |
| children | 9ad744d0804b |
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--- a/metilene.xml Thu Dec 10 16:02:17 2015 -0500 +++ b/metilene.xml Thu Dec 17 17:09:39 2015 -0500 @@ -1,133 +1,103 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="metilene" name="metilene" version="0.2-4.4"> +<tool id="metilene" name="metilene" version="0.2-4.0"> <description> - calling differentially methylated regions from - bisulfite sequencing data + calling differentially methylated regions from bisulfite sequencing data </description> - <requirements> - <requirement type="binary">Rscript</requirement> - <requirement type="package" version="5.18.1" >perl</requirement> - <requirement type="package" version="3.2.1" >R</requirement> - <requirement type="package" version="2.24" >bedtools</requirement> - <requirement type="package" version="0.2-4" >metilene</requirement> + <requirement type="package" version="0.2-4">metilene</requirement> + <requirement type="package" version="5.18.1">perl</requirement> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="0.9.3">r_ggplot2</requirement> + <requirement type="package" version="2.24">bedtools</requirement> <requirement type="package" version="8.22">gnu_coreutils</requirement> </requirements> - <stdio> <exit_code range=":-1"/> <exit_code range="1:" /> </stdio> - <version_command>echo "0.2-4"</version_command> - <command><![CDATA[ - ## =============== preprocessing - ## generate metilene_g1_g2.input from multiple bedgraph files - metilene_input.pl - --in1 $opt_in1 - ##echo ",".join(map(str,$opt_in1)) - --in2 $opt_in2 - ##echo ",".join(map(str,$opt_in2)) - >/dev/null 2>/dev/null - ; - ## =============== metilene main program - metilene - -M $Options.opt_M -m $Options.opt_m -d $Options.opt_d -t 1 -f 1 -v $Options.opt_v - metilene_g1_g2.input - >$output_bedlike - 2>/dev/null - ; - ## =============== postprocessing + ## preprocessing + ## generate metilene_g1_g2.input from multiple bedgraph files + metilene_input.pl + --in1 $opt_in1 + --in2 $opt_in2 + >/dev/null 2>/dev/null + && + ## metilene main program + metilene + -M $Options.opt_M + -m $Options.opt_m + -d $Options.opt_d + -t 1 + -f 1 + -v $Options.opt_v + metilene_g1_g2.input + >$output_bedlike + 2>/dev/null + && + ## postprocessing cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null - ; - ## write to job directory ... - metilene_output.pl -q $output_bedlike -p 0.05 -o ./metilene >/dev/null 2>/dev/null - ; - ## ... and move to output files - mv metilene_qval.0.05.bedgraph $output_qval_bedgraph 2>/dev/null; - mv metilene_qval.0.05.out $output_qval_out 2>/dev/null; - mv metilene_qval.0.05.pdf $output_qval_pdf 2>/dev/null + && + ## write to job directory + metilene_output.pl + -q $output_bedlike + -p 0.05 + -o ./metilene >/dev/null 2>/dev/null ]]></command> - <inputs> <!-- input bedgraph files 1 --> - <param - name="opt_in1" - type="data" format="bed,bedgraph" multiple="true" - optional="false" + <param name="opt_in1" type="data" format="bed,bedgraph" multiple="true" label="Input group 1" help="set of sorted bedgraph input profiles of group 1" /> <!-- input bedgraph files 2 --> - <param - name="opt_in2" - type="data" format="bed,bedgraph" multiple="true" - optional="false" + <param name="opt_in2" type="data" format="bed,bedgraph" multiple="true" label="Input group 2" help="set of sorted bedgraph input profiles of group 2" /> <!-- Advanced parameters (folded) --> <section name="Options" title="Advanced Options" expanded="False"> - <param - name="opt_M" + <param name="opt_M" type="integer" value="300" label="The allowed nt distance between two CpGs within a DMR" - type="integer" - optional="false" - value="300" - help="-M, --maxdist"/> + help="-M, --maxdist"/> - <param - name="opt_m" + <param name="opt_m" type="integer" value="10" label="The minimum # of CpGs in a DMR" - type="integer" - optional="false" - value="10" - help="-m, --mincpgs"/> - - <param - name="opt_d" + help="-m, --mincpgs"/> + + <param name="opt_d" type="float" value="0.1" label="The minimum mean methylation difference for calling DMRs" - type="float" - optional="false" - value="0.1" - help="-d, --minMethDiff"/> + help="-d, --minMethDiff"/> - <param - name="opt_v" - label="Stringency of the valley filter (0.0 - 1.0)" - type="float" - optional="false" - value="0.7" - help="-v, --valley"> - <validator type="in_range" min="0.0" max="1.0" - message="Valley filter value must be in [0,1]." /> - </param> - </section> + <param name="opt_v" type="float" value="0.7" label="Stringency of the valley filter (0.0 - 1.0)" + help="-v, --valley"> + <validator type="in_range" min="0.0" max="1.0" message="Valley filter value must be in [0,1]." /> + </param> + </section> </inputs> - <outputs> <!-- finally: for bed-like use format=tabular --> <data format="tabular" name="output_bedlike" label="${tool.name} on ${on_string}" /> <data format="bedgraph" name="output_bedgraph" - label="${tool.name} on ${on_string}" /> + label="${tool.name} bedgraph on ${on_string}" /> <data format="bedgraph" name="output_qval_bedgraph" - label="${tool.name} qval<0.05 bedgraph on ${on_string}" /> + label="${tool.name} qval<0.05 bedgraph on ${on_string}" + from_work_dir="metilene_qval.0.05.bedgraph" /> <data format="pdf" name="output_qval_pdf" - label="${tool.name} qval<0.05 plots on ${on_string}" /> + label="${tool.name} qval<0.05 plots on ${on_string}" + from_work_dir="metilene_qval.0.05.pdf" /> <data format="bedgraph" name="output_qval_out" - label="${tool.name} qval<0.05 out on ${on_string}" /> + label="${tool.name} qval<0.05 out on ${on_string}" + from_work_dir="metilene_qval.0.05.out" /> </outputs> - <tests> <test> - <param name="opt_in1" value="example_S1.bedgraph,example_S2.bedgraph,example_S3.bedgraph,example_S4.bedgraph" /> + <param name="opt_in1" value="example_S1.bedgraph,example_S2.bedgraph,example_S3.bedgraph,example_S4.bedgraph" /> <param name="opt_in2" value="example_S5.bedgraph,example_S6.bedgraph,example_S7.bedgraph,example_S8.bedgraph" /> - <output name="output_bedlike" file="metilene.out" /> + <output name="output_bedlike" file="metilene.out" /> </test> </tests> - - <help><![CDATA[ **Fast and sensitive calling of differentially methylated regions from bisulfite sequencing data** @@ -141,18 +111,17 @@ <citations> <citation type="bibtex">@Article{Juhling_Kretzmer_Bernhart-metil_Fast_and-2015, - author = {Juhling, Frank and Kretzmer, Helene and Bernhart, Stephan + author = {Juhling, Frank and Kretzmer, Helene and Bernhart, Stephan H. and Otto, Christian and Stadler, Peter F. and Hoffmann, Steve}, - title = {metilene: {Fast} and sensitive calling of differentially + title = {metilene: {Fast} and sensitive calling of differentially methylated regions from bisulfite sequencing data}, page = {[Epub ahead of print]}, - journal = {Genome Res}, - year = {2015}, - pmid = {26631489}, - doi = {10.1101/gr.196394.115}, - issn = {1088-9051}, - issn = {1549-5469}}</citation> + journal = {Genome Res}, + year = {2015}, + pmid = {26631489}, + doi = {10.1101/gr.196394.115}, + issn = {1088-9051}, + issn = {1549-5469}}</citation> </citations> - </tool>