view misp.xml @ 0:87f7630ab82f draft default tip

Imported from capsule None

<tool name="MISP: Motif-based Interval Screener with PSSM" id="misp" version="0.1.0">
  <description>Input one or more motifs, find all hits in peak regions</description>
  <requirements>
    <requirement type="package" version="2013-11-28">misp</requirement>
    <requirement type="package" version="2.19.1">bedtools</requirement>
  </requirements>
  <command>
#if $motifopt.motifopt_select == "upload"
  #set $motif_db = str($motifopt.motif_file)
#else
  #set $motif_db = "\${MISP_DATABASE_PATH}/motif/cistrome.db"
#end if
#set $motif_id = str($motifopt.motif_id)
#if $refGenomeSource.genomeSource == "history":
  #set $genome_file = $refGenomeSource.ownFile
#else:
  #set $genome_file = $refGenomeSource.index.fields.path
#end if
bedtools getfasta -fi $genome_file -bed $bedfile -fo out.fasta > /dev/null &amp;&amp;
misp out.fasta $motif_db $pvalue $motif_id output &amp;> $log  &amp;&amp;
cat output* > $outputtxt
  </command>
  <stdio>
    <exit_code range="1:" level="fatal" description="Error" />
  </stdio>
  <inputs>
     <param format="bed" name="bedfile" type="data" label="bed file for regions">
       <validator type="unspecified_build" />
     </param>
    <conditional name="refGenomeSource">
      <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options">
        <option value="cached" selected="True">Use a built-in genome</option>
        <option value="history">Use a genome from history</option>
      </param>
      <when value="cached">
        <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
          <options from_data_table="all_fasta">
            <filter type="data_meta" ref="bedfile" key="dbkey" column="1" multiple="True" separator="," />
            <validator type="no_options" message="No reference build available for selected input" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
      </when>  <!-- history -->
    </conditional>  <!-- refGenomeSource -->
     <conditional name="motifopt">
       <param name="motifopt_select" type="select" label="upload a motif or select from our database.">
         <option value="upload">Use uploaded motif</option>
         <option value="database">Use motif in cistrome database.</option>
       </param>
       <when value="upload">
         <param name="motif_file" type="data" label="motif file" />
         <param name="motif_id" type="text" label="The motif id in uploaded motif file. Or write 'all' to run all motifs in the file." />
       </when>
       <when value="database">
         <param name="motif_id" type="text" label="The motif id in Cistrome motif collection. Or write 'all' to run all motifs in the file." />
       </when>
     </conditional>
     <param name="pvalue" type="float" label="p-value cutoff for the motif screen" value="0.001">
      	<validator type="in_range" max="1" min="0" message="pvalue is out of range, width has to be between 0 to 1" />
     </param>
  </inputs>
  <outputs>
     <data format="txt" name="outputtxt" label="MISP hits on ${bedfile.name}"/>
     <data format="txt" name="log" label="Log of MISP on ${bedfile.name}"/>     
  </outputs>
  <tests>
    <test>
      <param name="bedfile" type="bed" value="test.bed" dbkey="mm9"/>
      <param name="genomeSource" value="history" />
      <param name="ownFile" type="fasta" value="mm9_chr19_part.fasta" dbkey="mm9"/>
      <param name="motifopt_select" value="upload" />
      <param name="motif_file" value="misp_motif" />
      <param name="motif_id" value="M00139" />
      <param name="pvalue" value="0.001" />
      <output name="outputtxt" file="misp.hits"/>
      <output name="log" file="misp.log"/>
    </test>
  </tests>
  <help>
Given a motif, this tool will find all hits of the motif in specified region.

-----

**Formula**

.. image:: ./static/cistrome_icons/misp_formula.png

-----

**TIP:** The source code of misp is available at bitbucket_

.. _bitbucket: https://bitbucket.org/hanfeisun/misp/overview


**TIP:** To check the motif id in our database, click here_

.. _here: http://cistrome.org/motif/

-----

Left to right shoule be:

T

C

G

A

**Example of the format of uploaded motif database.**

M00139

0.667 0.111 0.667 0.01 0.01 0.01 0.01 0.01 0.333 0.01 0.01 0.333 0.444 0.222 0.01 0.01 0.01 0.01

0.01 0.546 0.111 0.97 0.01 0.97 0.01 0.97 0.111 0.01 0.444 0.444 0.536 0.333 0.222 0.111 0.01 0.222

0.01 0.333 0.111 0.01 0.01 0.01 0.97 0.01 0.222 0.01 0.536 0.111 0.01 0.333 0.758 0.556 0.667 0.667

0.313 0.01 0.111 0.01 0.97 0.01 0.01 0.01 0.334 0.97 0.01 0.112 0.01 0.112 0.01 0.323 0.313 0.101

hPDI060

0.01 0.01 0.01 0.625 0.01 0.01

0.97 0.97 0.97 0.01 0.5 0.97

0.01 0.01 0.01 0.01 0.48 0.01

0.01 0.01 0.01 0.355 0.01 0.01
  </help>

</tool>