comparison deseq2.xml @ 14:d0c39b5e78cf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e811a7887db870f4f94f620f52bce656c8d5ba23

13:3660c9088494

            </repeat>
        </repeat>

        <conditional name="tximport">
            <param name="tximport_selector" type="select" label="Choice of Input data">
                <option value="count" selected="True">Count data (e.g. from HTSeq-count or featureCounts)</option>
                <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
            </param>
            <when value="tximport">
                <param name="txtype" type="select" label="Program used to generate TPMs">
                    <option value="kallisto">kallisto</option>

**Inputs**

**Count Files**

DESeq2_ takes count tables generated from **featureCounts** or **HTSeq-count** as input. Count tables must be generated for each sample individually. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.

The following table gives some examples of factors and their levels:

========= ============== ===============
Factor    Factor level 1 Factor level 2

14:d0c39b5e78cf

            </repeat>
        </repeat>

        <conditional name="tximport">
            <param name="tximport_selector" type="select" label="Choice of Input data">
                <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
                <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
            </param>
            <when value="tximport">
                <param name="txtype" type="select" label="Program used to generate TPMs">
                    <option value="kallisto">kallisto</option>

**Inputs**

**Count Files**

DESeq2_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually, should have no header rows, and rows should be in the same order. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.

The following table gives some examples of factors and their levels:

========= ============== ===============
Factor    Factor level 1 Factor level 2