Mercurial > repos > tyty > structurefold
diff predict/predict_RNAs.xml @ 59:afd114ef8857 draft
Uploaded
author | tyty |
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date | Tue, 18 Nov 2014 01:01:52 -0500 |
parents | 12551ae128be |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/predict/predict_RNAs.xml Tue Nov 18 01:01:52 2014 -0500 @@ -0,0 +1,59 @@ +<tool id="predict_pipeline" name="RNA Structure Prediction" version="1.0"> + <description></description> + <command interpreter="python">predict_RNAs.py $rna_list $reference_file $reactivity_file $output </command> + <requirements> + <requirement type="package" version="1.61">biopython</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="1.2.1">matplotlib</requirement> + </requirements> + <inputs> + <param name="rna_list" type="data" format="txt" label="List of RNA ids to predict"/> + <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/> + <param name="reactivity_file" type="data" optional = "true" label="Reactivity file"/> + + </inputs> + <outputs> + <data name="output" format=".tgz"/> + </outputs> + <tests> + <test> + <param name="rna_list" value="id_list_test.txt" /> + <param name="reference_file" value="cdna.txt" /> + <param name="reactivity_file" value="mRNA_react_test2.txt" /> + <output name="output" file="structures.out" /> + </test> + </tests> + <help> + + +**TIPS**: + +----- + +**Input**: + +* 1. A file with transcript Ids (Max num. 20), (each ID one line) +* 2. Reference file (fasta) used to map the reads to +* [Optional]: +* 1. A reactivity file with structural reactivity for each nucleotide on the sequence provided + +----- + +**Output**: + +* 1. .ct files with predicted RNA structures [transciptID.ct] +* 2. .ps files which depict the predicted RNA structures [[transciptID.ps] +* [Optional] +* 3. .png files that shows the distribution of the reactivity of each nucleotide on the transcripts of interest. [transciptID.png] +* 4. A .txt file that includes the reactivities of all the nucleotides on the transcripts of interest. [transciptID.txt] + +----- + +**Attention** + +Make sure any of the transcript Ids does not contain "|" or space! + + + + </help> +</tool>