comparison footprint.xml @ 1:0d94a529f925 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 6767a5ffb02052c844e9d862c79912f998f39d8e

0:4bff424dfa47

<?xml version="1.0" encoding="UTF-8"?>
<tool id="footprint" name="footprint" version="1.0.0">
    <requirements>
        <requirement type="package" version="1.0.0">footprint</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
            ln -s '$bam_file' ./bam_file.bam

            &&

            find_footprints.sh

            ./bam_file.bam

            '$chrom_sizes'

            '$motif_coords'

            ## genome source
            #if $refGenomeSource.genomeSource == "history":
                '$refGenomeSource.ownFile'
            #else
                '$refGenomeSource.builtin.fields.path'
            #end if

            $factor_name

            '$bias_file'

            '$peak_file'

            $no_of_components

            $background

            $fixed_bg

            &&
            mv *.PARAM PARAM
            &&
            mv *.RESULTS RESULTS
            &&
            mv *.plot2.png plot2.png
            &&
            mv *.plot1.png plot1.png
]]>
    </command>
    <inputs>
        <param name="bam_file" type="data" format="BAM" label="alignment bam file" help="" />
        <param name="chrom_sizes" type="data" format="tablular" label="chromosome length" help="" />

**Purpose**

This is a pipeline to find transcription factor footprints in ATAC-seq or DNase-seq data.


-----

.. class:: infomark

**Inputs**

coordinates of motif
 * A 6-column bed file with the coordinates of motif matches (eg resulting from scanning the genome with a PWM) for the transcription factor of interest.
 * The 6 columns should contain chromosome, start coordinate, end coordinate, name, score and strand information in this order. The coordinates should be closed (1-based).
 * Example: chr1    24782   24800   .       11.60   -

transcription factor
 * The name of the transcription factor of interest supplied by the user, e.g. CTCF.

cleavage/transposition bias

fixed background component
 * Whether the background component should be kept fixed.
 * Options are TRUE or FALSE.
 * Setting "TRUE" keeps this component fixed, whereas setting "FALSE" lets it be reestimated during training.

-----

.. class:: infomark

 * When 3 components are used, this plot shows the weighted average of the 2 footprint components as the final footprint profile.

]]></help>
    <citations>
        <citation type="bibtex">@ARTICLE{footprint,
        author = {Aslihan Karabacak and Uwe Ohler},
        title = {To submit},
        journal = {},
        year = {},
        volume = {},
        pages = {}

1:0d94a529f925

<?xml version="1.0" encoding="UTF-8"?>
<tool id="footprint" name="footprint" version="1.0.0">
    <requirements>
        <requirement type="package" version="1.0.0">footprint</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
ln -s '$bam_file' ./bam_file.bam
&&
find_footprints.sh
    ./bam_file.bam
    '$chrom_sizes'
    '$motif_coords'
    ## genome source
    #if $refGenomeSource.genomeSource == "history":
        '$refGenomeSource.ownFile'
    #else
        '$refGenomeSource.builtin.fields.path'
    #end if
    '$factor_name'
    '$bias_file'
    '$peak_file'
    $no_of_components
    $background
    $fixed_bg
    &&
mv *.PARAM PARAM &&
mv *.RESULTS RESULTS &&
mv *.plot2.png plot2.png &&
mv *.plot1.png plot1.png

]]>
    </command>
    <inputs>
        <param name="bam_file" type="data" format="BAM" label="alignment bam file" help="" />
        <param name="chrom_sizes" type="data" format="tablular" label="chromosome length" help="" />

**Purpose**

This is a pipeline to find transcription factor footprints in ATAC-seq or DNase-seq data.

-----

.. class:: infomark

**Inputs**

coordinates of motif
 * A 6-column bed file with the coordinates of motif matches (eg resulting from scanning the genome with a PWM) for the transcription factor of interest.
 * The 6 columns should contain chromosome, start coordinate, end coordinate, name, score and strand information in this order. The coordinates should be closed (1-based).
 * Example: chr1    24782   24800   .       11.60   -
 * There should not be any additional columns.

transcription factor
 * The name of the transcription factor of interest supplied by the user, e.g. CTCF.

cleavage/transposition bias

fixed background component
 * Whether the background component should be kept fixed.
 * Options are TRUE or FALSE.
 * Setting "TRUE" keeps this component fixed, whereas setting "FALSE" lets it be reestimated during training.
 * In general, if the background is estimated from bias (option "Seq"), it is recommended to keep it fixed.

-----

.. class:: infomark

 * When 3 components are used, this plot shows the weighted average of the 2 footprint components as the final footprint profile.

]]></help>
    <citations>
        <citation type="bibtex">@ARTICLE{footprint,
        author = {Aslihan Karabacak, Galip Gurkan Yardimci, Ricardo Wurmus, Dilmurat Yusuf, Uwe Ohler},
        title = {To submit},
        journal = {},
        year = {},
        volume = {},
        pages = {}