annotate preprocessing.xml @ 2:a9202b64f3bf draft

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty

<tool id="preproc" name="Preprocessing" version="0.1">
  <requirements>
    <requirement type="package" version="0.1.8">graphclust-wrappers</requirement>
  </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
		<![CDATA[

    'preprocessing.pl'
    '$fastaFile'  $max_length $in_winShift $min_seq_length

]]>
	</command>
    <inputs>
        <param type="data" name="fastaFile" format="fasta" />
        <param name="max_length" type="integer" value="10000" size="5" label="window size"/>
        <param name="in_winShift" type="integer" value="100" size="5" label="window shift in percent"/>
        <param name="min_seq_length" type="integer" value="5" size="5" label="minimum sequence length"/>
    </inputs>

    <outputs>
        <data name="data.fasta" format="fasta" from_work_dir="FASTA/data.fasta" label="data.fasta"/>
        <data name="data.map" format="txt" from_work_dir="FASTA/data.map" label="data.map"/>
        <data name="data.names" format="txt" from_work_dir="FASTA/data.names" label="data.names"/>
        <data name="data.fasta.scan" format="fasta" from_work_dir="FASTA/data.fasta.scan" label="data.fasta.scan"/>
        <data name="FASTA" format="zip" from_work_dir="FASTA.zip" label="FASTA.ZIP"/>
    </outputs>


    <tests>
    <test>
        <param name="fastaFile" value="input.fa"/>
        <param name="max_length" value="10000"/>
        <param name="in_winShift" value="100"/>
        <param name="min_seq_length" value="5"/>
        <output name="data.fasta" file="FASTA/data.fasta"/>
        <output name="data.map" file="FASTA/data.map" />
        <output name="data.names" file="FASTA/data.names"/>
        <output name="data.fasta.scan" file="FASTA/data.fasta.scan" />
    </test>
</tests>

    <help>
<![CDATA[

**What it does**

The tool takes as an input file of sequences in Fasta format and creates the final input for GraphCLust based on given parameters.

**Parameters**

+ **window size** : All input sequences are splitted into fragments of this length.
  The shift of the sliding window can be defined via option *window shift in percent*.
  This paramter reflects the expected length of signals to be found.
  Slightly larger windows are usually ok. Too small windows can disturb existing signals.




+ **window shift in percent** : Relative window size in % for window shift during input preprocessing.
  Please note that a small shift results in much more fragments for clustering. The benefit is that RNA
  motifs/structures are not destroyed by arbitrary split points. Smaller
  shifts usually increase the cluster quality. Too small shifts (<20) are not
  recommended as a dense center is "polluted" by overlapping fragments and
  no other occurences in the dataset can be found.





+ **minimum sequence length** : Minimal length of input sequences.
  Every input sequence below that length is ignored completely during clustering.


    ]]></help>


    <citations>
        <citation type="doi">10.1093/bioinformatics/bts224</citation>
    </citations>


</tool>