| Previous changeset 0:4ad5a728b517 (2015-02-10) |
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Commit message:
Uploaded |
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added:
fastaptamer_enrich_1.xml |
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| diff -r 4ad5a728b517 -r 748195d5c4de fastaptamer_enrich_1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastaptamer_enrich_1.xml Tue Feb 10 14:49:10 2015 -0500 |
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| @@ -0,0 +1,58 @@ +<tool id="fastaptamer_enrich_1_0_2" name="FASTAptamer-Enrich" version="1.0.2"> + + <description>Calculate fold-enrichment of each sequence across populations</description> + + <version_command>fastaptamer_enrich -v</version_command> + + <command interpreter="perl">fastaptamer_enrich -x $input_x -y $input_y -o $output -f $filter + # if str(input_z) != '' + -z "${input_z}" + # end if + </command> + + <inputs> + <param name="input_x" type="data" format="fasta" label="Input file X" help="Must use FASTA output from FASTAptamer-Count or FASTAptamer-Cluster"></param> + <param name="input_y" type="data" format="fasta" label="Input file Y" help="Must use FASTA output from FASTAptamer-Count or FASTAptamer-Cluster"></param> + <param name="input_z" type="data" format="fasta" optional="true" label="Input file Z" help="Must use FASTA output from FASTAptamer-Count or FASTAptamer-Cluster"></param> + <param name="filter" type="float" optional="true" value="0" label="RPM Threshold Filter" help="Sequences with an aggregate RPM (across all populations) less than supplied value will be excluded from analysis"></param> + </inputs> + + <outputs> + <data name="output" format="tabular" label="FASTAptamer-Enrich output file"></data> + </outputs> + + <help> + +.. class:: warningmark + +FASTAptamer-Enrich requires FASTA formatted input files generated by FASTAptamer-Count or FASTAptamer-Cluster. + +------ + +**FASTAptamer-Enrich** rapidly calculates "fold-enrichment" values for each sequence across two or three input files. Output is provided as a tab-delimited file and is formatted to include sequence composition, length, rank, reads, reads per million (RPM), cluster information (if available) and enrichment values for each sequence. + +An optional threshold filter can be applied to exclude sequences with total reads per million (across all input populations) less than the number supplied. + +Enrichment is calculated by dividing reads per million of y/x (and z/y and z/x, if a third input file is specified). + +------ + +.. image:: + http://burkelab.missouri.edu/images/fastaptamer-logo-xs.png + :height: 98 + :width: 300 + +For more information on FASTAptamer, visit our website_. + +FASTAptamer is distributed under a GNU GPL v3.0 license. For complete license click here_. + +.. _here: http://burkelab.missouri.edu/fastaptamer/LICENSE.txt +.. _website: http://burkelab.missouri.edu/fastaptamer.html + + </help> + + <citations> + <citation type="doi">doi:10.1038/mtna.2015.4</citation> + </citations> + +</tool> |