Mercurial > repos > tyty > structurefold
diff reactivity_cal/reactivity_calculation.xml @ 63:c1f1b552c1b8 draft
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author | tyty |
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date | Tue, 18 Nov 2014 15:54:11 -0500 |
parents | 765da0718336 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reactivity_cal/reactivity_calculation.xml Tue Nov 18 15:54:11 2014 -0500 @@ -0,0 +1,60 @@ +<tool id="react_cal_pipeline" name="Reactivity Calculation" version="1.0"> + <description></description> + <command interpreter="python">react_cal.py $dist_file1 $dist_file2 $seq_file $nt_spec $flag_in $threshold $output </command> + <requirements> + <requirement type="package" version="1.61">biopython</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + </requirements> + <inputs> + <param name="dist_file1" type="data" format="txt" label="RTSC file for (+) library"/> + <param name="dist_file2" type="data" format="txt" label="RTSC file for (-) library"/> + <param name="seq_file" type="data" format="fasta" label="Reference genome/transcriptome"/> + <param name="nt_spec" type="select" label="Nucleotide specificity"> + <option value="AC">AC</option> + <option value="ATCG">AUCG</option> + </param> + <param name="flag_in" type="boolean" checked="true" truevalue = "1" falsevalue = "0" label="Normalization is performed if checked"/> + <param name="threshold" type="float" value = "7" optional = "true" label="Threshold to cap the reactivities"/> + </inputs> + <outputs> + <data name="output" format="txt"/> + </outputs> + <tests> + <test> + <param name="dist_file1" value="dis_f_N1Ap_rrna.txt" /> + <param name="dist_file2" value="dis_f_N1Am_rrna.txt" /> + <param name="seq_file" value="rRNA.txt" /> + <param name="nt_spec" value="AC" /> + <param name="flag_in" value="1" /> + <param name="threshold" value="7" /> + <output name="output" file="DMS_reactivities.out" /> + + </test> + </tests> + + <help> + + +**TIPS**: + +----- + +**Input**: + +* 1. RTSC files (Output of Get RT Stop Counts) for (+) and (-) library +* 2. Reference file (fasta) used to map the reads to +* 3. Nucleotide Specificity (Type of nucleotides to have reactivity, e.g. AC for DMS and ACTG for SHAPE) +* [Optional]: +* 1. A threshold to cap the structural reactivities. {Default: 7} +* 2. Flag that determines whether to perform 2%-8% normalization {Default: Yes} + +----- + +**Output**: + +A text file with structural reactivity for each nucleotide (Reactivity file) + + + + </help> +</tool>