Mercurial > repos > cafletezbrant > kmersvm
view kmersvm/seqprofile.xml @ 0:7fe1103032f7 draft
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author | cafletezbrant |
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date | Mon, 20 Aug 2012 18:07:22 -0400 |
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<tool id="kmersvm_seqprofile" name="Sequence Profiles"> <description>provide length, gc content, and repeat fraction of each sequence</description> <command interpreter="python">scripts/make_profile.py $input $dbkey ${indices_path.fields.path} seq_profile.txt</command> <inputs> <param format="interval" name="input" type="data" label="BED File of Regions of interest" /> <validator type="unspecified_build" /> <validator type="dataset_metadata_in_file" filename="nullseq_indices.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are currently unavailable for the specified build." /> <param name="indices_path" type="select" label="Available Datasets"> <options from_file="nullseq_indices.loc"> <column name="dbkey" index="0"/> <column name="value" index="0"/> <column name="name" index="1"/> <column name="path" index="2"/> <filter type="data_meta" ref="input" key="dbkey" column="0" /> </options> </param> </inputs> <outputs> <data format="tabular" name="seq_profile.txt" from_work_dir="seq_profile.txt" /> </outputs> <help> **What it does** Takes as input a BED file and the file's corresponding genome build. Returns length, GC and repeat content information for each interval in bed file. ---- **Example** Profile file:: mm9_chr10_6238300_6238926_+ 626 0.525559105431 0.0 mm9_chr10_7757450_7758801_+ 1351 0.451517394523 0.0384900074019 mm9_chr10_8992150_8992551_+ 401 0.411471321696 0.0 mm9_chr10_9265550_9266026_+ 476 0.38025210084 0.0 </help> </tool>