annotate reactivity_cal/reactivity_calculation.xml @ 79:8ec9acab68ab draft

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<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>