comparison ctat_metagenomics.xml @ 2:e5182440ba17 draft

Trying to fix problems with ctat_star_fusion and ctat_metagenomics.

1:1c8d5eb15ed1

<tool id="ctat_metagenomics" name="ctat_metagenomics" version=1.0.0 profile="17.05">

    <description>Centrifuge - Classifier for metagenomic sequences (RNA-Seq)</description>
    <requirements>
        <requirement type="package" version="1.0.1">ctat-metagenomics</requirement>
    </requirements>

                </conditional>
            </when>
        </conditional>

        <param name="index" type="select" label="Choose reference genome index :" help="Select genome index">
            <options from_data_table="ctat_centrifuge_indexes">
        </param>
      
    </inputs>

    <outputs>

                </assert_contents>
            </output>
            <output name="classification_report" file="centrifuge/SRR2219890_1.classification.report.txt" />
            <output name="kraken_style_report" file="centrifuge/SRR2219890_1.kraken_style_report.txt" />
        </test>
        <test>
            <!-- The following test uses two files that are left/right paired reads.
            -->
            <param name="format" value="fastq" />
            <param name="type" value="paired" />
            <param name="left_fq" value="centrifuge/SRR073747_1.fastq" />
            <param name="right_fq" value="centrifuge/SRR073747_2.fastq" />
            <!-- FIX - How are we going to set the index value when we don't know what is in the table? How do we find it for testing?
            <param name="index.fields.path" value="/N/dc2/projects/galaxyshared/trinity/dev/Trinity_CTAT/metagenomics/phv" />
            -->
            <output name="classification_results" >
                <assert_contents>
                    <has_line_matching expression=".+" />
                    <has_line line="readID&#009;seqID&#009;taxID&#009;score&#009;2ndBestScore&#009;hitLength&#009;queryLength&#009;numMatches" />
                </assert_contents>
            </output>
            <output name="classification_report" file="centrifuge/SRR073747_1_2.classification.report.txt" />
            <output name="kraken_style_report" file="centrifuge/SRR073747_1_2.kraken_style_report.txt" />
        </test>
        <test>
            <!-- The following test uses an unpaired Trinity fasta file.
            -->
            <param name="format_type.format" value="fasta" />
            <param name="fasta_file" value="centrifuge/TrinitySRR2219890.fasta" />
            <!-- FIX - How are we going to set the index value when we don't know what is in the table? How do we find it for testing?
            <param name="index" value="/N/dc2/projects/galaxyshared/trinity/dev/Trinity_CTAT/metagenomics/phv" />
            -->
            <output name="classification_results" >
                <assert_contents>
                    <has_line_matching expression=".+" />
                    <has_line line="readID&#009;seqID&#009;taxID&#009;score&#009;2ndBestScore&#009;hitLength&#009;queryLength&#009;numMatches" />
                </assert_contents>
            </output>
            <output name="classification_report" file="centrifuge/TrinitySRR2219890.classification.report.txt" />>
            <output name="kraken_style_report" file="centrifuge/TrinitySRR2219890.kraken_style_report.txt" />
        </test>
    </tests>

    <help>
.. class:: infomark
 

2:e5182440ba17

<tool id="ctat_metagenomics" name="ctat_metagenomics" version="1.0.0" profile="17.05">

    <description>Centrifuge - Classifier for metagenomic sequences (RNA-Seq)</description>
    <requirements>
        <requirement type="package" version="1.0.1">ctat-metagenomics</requirement>
    </requirements>

                </conditional>
            </when>
        </conditional>

        <param name="index" type="select" label="Choose reference genome index :" help="Select genome index">
            <options from_data_table="ctat_centrifuge_indexes" />
        </param>
      
    </inputs>

    <outputs>

                </assert_contents>
            </output>
            <output name="classification_report" file="centrifuge/SRR2219890_1.classification.report.txt" />
            <output name="kraken_style_report" file="centrifuge/SRR2219890_1.kraken_style_report.txt" />
        </test>
    </tests>

    <help>
.. class:: infomark