comparison salmonquant.xml @ 18:c6c81a918ae1 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"

17:c56d23a0a2a4

<tool id="salmon" name="Salmon quant" version="@VERSION@+galaxy1">
    <description>Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

                    <section name="s_index">
                        <param name="fasta" value="transcripts.fasta"/>
                    </section>
                </conditional>
                <section name="input">
                    <param name="single_or_paired.single_or_paired_opts" value="paired" />
                    <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />
                    <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />
                    <param name="single_or_paired.strandedness" value="U"/>
                </section>
                <param name="writeMappings" value="true"/>
            </conditional>
            <output name="output_quant" ftype="tabular">
                <assert_contents>

                    <has_text text="NM_153693" />
                    <has_text text="NR_031764" />
                    <has_n_columns n="5" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="quant_type">
                <param name="qtype" value="reads"/>
                <conditional name="refTranscriptSource">

                <param name="sampleOut" value="--sampleOut"/>
                <param name="sampleUnaligned" value="--sampleUnaligned"/>
                <param name="noErrorModel" value="--noErrorModel"/>
                <param name="numErrorBins" value="5"/>
            </conditional>
            <output name="postSample" ftype="bam" value="postSample.bam"/>
            <assert_stderr>
                <has_text text="Sampling alignments; outputting results to ./output/postSample.bam"/>
            </assert_stderr>
        </test>
        <test expect_num_outputs="1">
            <conditional name="quant_type">
                <param name="qtype" value="reads"/>
                <conditional name="refTranscriptSource">

18:c6c81a918ae1

<tool id="salmon" name="Salmon quant" version="@VERSION@+@GALAXY_VERSION@" profile="@PROFILE_VERSION@">
    <description>Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

                    <section name="s_index">
                        <param name="fasta" value="transcripts.fasta"/>
                    </section>
                </conditional>
                <section name="input">
                    <conditional name="single_or_paired">
                        <param name="single_or_paired_opts" value="paired" />
                        <param name="input_mate1" value="fastqs/reads_1.fastq" />
                        <param name="input_mate2" value="fastqs/reads_2.fastq" />
                        <conditional name="libtype">
                            <param name="strandedness" value="U"/>
                        </conditional>
                    </conditional>
                </section>
                <param name="writeMappings" value="true"/>
            </conditional>
            <output name="output_quant" ftype="tabular">
                <assert_contents>
                    <has_text text="EffectiveLength" />
                    <has_text text="TPM" />
                    <has_text text="NM_001168316" />
                    <has_text text="NM_174914" />
                    <has_text text="NM_018953" />
                    <has_text text="NR_003084" />
                    <has_text text="NM_017410" />
                    <has_text text="NM_153693" />
                    <has_text text="NR_031764" />
                    <has_n_columns n="5" />
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="--libType IU"/>
            </assert_command>
        </test>
        <test expect_num_outputs="2">
            <conditional name="quant_type">
                <param name="qtype" value="reads"/>
                <conditional name="refTranscriptSource">
                    <param name="TranscriptSource" value="history"/>
                    <section name="s_index">
                        <param name="fasta" value="transcripts.fasta"/>
                    </section>
                </conditional>
                <section name="input">
                    <param name="single_or_paired.single_or_paired_opts" value="paired" />
                    <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />
                    <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />
                </section>
                <param name="writeMappings" value="true"/>
            </conditional>
            <output name="output_quant" ftype="tabular">
                <assert_contents>

                    <has_text text="NM_153693" />
                    <has_text text="NR_031764" />
                    <has_n_columns n="5" />
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="--libType A"/>
            </assert_command>
        </test>
        <test expect_num_outputs="1">
            <conditional name="quant_type">
                <param name="qtype" value="reads"/>
                <conditional name="refTranscriptSource">

                <param name="sampleOut" value="--sampleOut"/>
                <param name="sampleUnaligned" value="--sampleUnaligned"/>
                <param name="noErrorModel" value="--noErrorModel"/>
                <param name="numErrorBins" value="5"/>
            </conditional>
            <!-- bam output uses non-deterministic sampling, so can only use compare="sim_size" -->
            <output name="postSample" ftype="bam" value="postSample.bam" compare="sim_size" delta="20000"/>
            <assert_stderr>
                <has_text text="Sampling alignments; outputting results to ./output/postSample.bam"/>
            </assert_stderr>
        </test>
        <test expect_num_outputs="2">
            <conditional name="quant_type">
                <param name="qtype" value="alignment"/>
                <param name="afile" value="salmonbam.bam"/>
                <param name="ont" value="true" />
                <param name="transcript" value="transcripts.fasta"/>
                <param name="sampleOut" value="--sampleOut"/>
                <param name="sampleUnaligned" value="--sampleUnaligned"/>
                <param name="noErrorModel" value="--noErrorModel"/>
                <param name="numErrorBins" value="5"/>
            </conditional>
            <assert_stderr>
                <has_text text="Sampling alignments; outputting results to ./output/postSample.bam"/>
            </assert_stderr>
            <assert_command>
                <has_text text=" --ont "/>
            </assert_command>
        </test>
        <test expect_num_outputs="1">
            <conditional name="quant_type">
                <param name="qtype" value="reads"/>
                <conditional name="refTranscriptSource">