Mercurial > repos > tyty > structurefold
comparison predict/predict_RNAs.xml @ 59:afd114ef8857 draft
Uploaded
| author | tyty |
|---|---|
| date | Tue, 18 Nov 2014 01:01:52 -0500 |
| parents | 12551ae128be |
| children |
comparison
equal
deleted
inserted
replaced
| 58:971ef91f6b68 | 59:afd114ef8857 |
|---|---|
| 1 <tool id="predict_pipeline" name="RNA Structure Prediction" version="1.0"> | |
| 2 <description></description> | |
| 3 <command interpreter="python">predict_RNAs.py $rna_list $reference_file $reactivity_file $output </command> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="1.61">biopython</requirement> | |
| 6 <requirement type="package" version="1.7.1">numpy</requirement> | |
| 7 <requirement type="package" version="1.2.1">matplotlib</requirement> | |
| 8 </requirements> | |
| 9 <inputs> | |
| 10 <param name="rna_list" type="data" format="txt" label="List of RNA ids to predict"/> | |
| 11 <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/> | |
| 12 <param name="reactivity_file" type="data" optional = "true" label="Reactivity file"/> | |
| 13 | |
| 14 </inputs> | |
| 15 <outputs> | |
| 16 <data name="output" format=".tgz"/> | |
| 17 </outputs> | |
| 18 <tests> | |
| 19 <test> | |
| 20 <param name="rna_list" value="id_list_test.txt" /> | |
| 21 <param name="reference_file" value="cdna.txt" /> | |
| 22 <param name="reactivity_file" value="mRNA_react_test2.txt" /> | |
| 23 <output name="output" file="structures.out" /> | |
| 24 </test> | |
| 25 </tests> | |
| 26 <help> | |
| 27 | |
| 28 | |
| 29 **TIPS**: | |
| 30 | |
| 31 ----- | |
| 32 | |
| 33 **Input**: | |
| 34 | |
| 35 * 1. A file with transcript Ids (Max num. 20), (each ID one line) | |
| 36 * 2. Reference file (fasta) used to map the reads to | |
| 37 * [Optional]: | |
| 38 * 1. A reactivity file with structural reactivity for each nucleotide on the sequence provided | |
| 39 | |
| 40 ----- | |
| 41 | |
| 42 **Output**: | |
| 43 | |
| 44 * 1. .ct files with predicted RNA structures [transciptID.ct] | |
| 45 * 2. .ps files which depict the predicted RNA structures [[transciptID.ps] | |
| 46 * [Optional] | |
| 47 * 3. .png files that shows the distribution of the reactivity of each nucleotide on the transcripts of interest. [transciptID.png] | |
| 48 * 4. A .txt file that includes the reactivities of all the nucleotides on the transcripts of interest. [transciptID.txt] | |
| 49 | |
| 50 ----- | |
| 51 | |
| 52 **Attention** | |
| 53 | |
| 54 Make sure any of the transcript Ids does not contain "|" or space! | |
| 55 | |
| 56 | |
| 57 | |
| 58 </help> | |
| 59 </tool> |