comparison oases_optimiser.xml @ 2:ab37eb09b4ca draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/oases commit d5a2de4b4c556e028fc5ef7ffcc7c2d0cf31c5ec

1:c9b5ec6c45e8

<tool id="oasesoptimiserv" name="Oases_optimiser" version="1.3.0">
    <description>Auto optimise de novo RNA-seq Oases/Velvet assembly</description>
    <requirements>
        <requirement type="package" version="0.2.09">oases</requirement>
        <requirement type="package" version="1.2.10">velvet</requirement>
        <requirement type="package" version="3.7.6">python</requirement>
    </requirements>
    <command><![CDATA[
	python "$__tool_directory__"/oases_optimiser.py  "$start_hash_length" "$end_hash_length"
	#for $i in $inputs
		"${i.input}"
    #end for
	"$transcripts"
	]]></command>
    <inputs>
        <param label="Start Hash Length" name="start_hash_length" type="select" help="k-mer length in base pairs of the words being hashed. Shorter hash lengths (i.e. less than 31) may cause out-of-memory problems.">
            <option value="11" selected="yes">11</option>
            <option value="13">13</option>
            <option value="15">15</option>

                    <has_line_matching expression=">Locus_25_Transcript_1/1_Confidence_.+" />
                </assert_contents>
            </output>
        </test>
    </tests>
	<help>
**Oases Optimiser Overview**

Oases_ is a de novo transcriptome assembler specially designed to work with short reads. It is an extension of Velvet developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.

Provide all the information about insert lengths and their standard deviation as

Oases produces a number of output files, which correspond to the different algorithms
being run succesively on the data. In the above example, you would find:

transcripts.fa
	A FASTA file containing the transcripts imputed directly from trivial
	clusters of contigs (loci with less than two transcripts and Confidence Values = 1)
	and the highly expressed transcripts imputed by dynamic
	programming (loci with more than 2 transcripts and Confidence Values less than 1).

splicing_events.txt
	A hybrid file which describes the contigs contained in each locus in FASTA
	format, interlaced with one line descriptions of splicing events using the
	AStalavista nomenclature*.

Read the Oases `documentation`__ for details on using the Oases Assembler.

.. _Oases: http://www.ebi.ac.uk/~zerbino/oases/

.. __: http://www.ebi.ac.uk/~zerbino/oases/Manual.txt

------

**Other outputs (as per Velvet)**

2:ab37eb09b4ca

<tool id="oasesoptimiserv" name="Oases_optimiser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Auto optimise de novo RNA-seq Oases/Velvet assembly</description>
    <macros>
        <token name="@TOOL_VERSION@">1.4.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">23.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="0.2.09">oases</requirement>
        <requirement type="package" version="1.2.10">velvet</requirement>
        <requirement type="package" version="3.12.1">python</requirement>
    </requirements>
    <command><![CDATA[
    python '$__tool_directory__/oases_optimiser.py' '$start_hash_length' '$end_hash_length'
    #for $i in $inputs
        '${i.input}'
    #end for
    '$transcripts'
    ]]></command>
    <inputs>
        <param label="Start Hash Length" name="start_hash_length" type="select" help="k-mer length in base pairs of the words being hashed. Shorter hash lengths (i.e. less than 31) may cause out-of-memory problems.">
            <option value="11" selected="yes">11</option>
            <option value="13">13</option>
            <option value="15">15</option>

                    <has_line_matching expression=">Locus_25_Transcript_1/1_Confidence_.+" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
**Oases Optimiser Overview**

Oases_ is a de novo transcriptome assembler specially designed to work with short reads. It is an extension of Velvet developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.

Provide all the information about insert lengths and their standard deviation as

Oases produces a number of output files, which correspond to the different algorithms
being run succesively on the data. In the above example, you would find:

transcripts.fa
    A FASTA file containing the transcripts imputed directly from trivial
    clusters of contigs (loci with less than two transcripts and Confidence Values = 1)
    and the highly expressed transcripts imputed by dynamic
    programming (loci with more than 2 transcripts and Confidence Values less than 1).

splicing_events.txt
    A hybrid file which describes the contigs contained in each locus in FASTA
    format, interlaced with one line descriptions of splicing events using the
    AStalavista nomenclature*.

Read the Oases `documentation`__ for details on using the Oases Assembler.

.. _Oases: https://github.com/dzerbino/oases

.. __: https://bioweb.pasteur.fr/docs/modules/oases/0.2.08/OasesManual.pdf

------

**Other outputs (as per Velvet)**