comparison stacks_gstacks.xml @ 5:aa645d419016 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f

4:285e1f85c11a

                <option value="marukilow" selected="true">marukilow</option>
                <option value="marukihigh">marukihigh</option>
                <option value="snp">snp</option>
            </param>
            <when value="marukilow">
                <expand macro="variant_calling_options_vg"/>
            </when>
            <when value="marukihigh">
                <expand macro="variant_calling_options_vg"/>
            </when>
            <when value="snp">

            <conditional name="mode_cond">
                <param name="mode_select" value="denovo"/>
            </conditional>
            <param name="add_log" value="yes" />
            <param name="add_log_distribs" value="yes" />
            <output name="output_log" ftype="txt" file="gstacks/gstacks.log" lines_diff="6"/>
            <output name="distribs" ftype="txt" file="gstacks/gstacks.log.distribs" compare="sim_size"/>
            <output_collection name="gstacks_out" type="list" count="2">
                <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="2"/>
                <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz"/>
            </output_collection>

                    <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" />
                </conditional>
            </conditional>
            <param name="model_cond|model" value="snp"/>
            <param name="model_cond|gt_alpha" value="0.1" />
            <param name="add_log" value="yes" />
            <assert_command>
                <not_has_text text="-I bam_inputs" />
                <has_text text="-B " />
                <has_text text="--unpaired" />

must be consistent if repeated different files.
Otherwise read groups are unneeded and ignored.

**Output files**

TODO

@STACKS_INFOS@
]]>
    </help>
    <expand macro="citation" />

5:aa645d419016

                <option value="marukilow" selected="true">marukilow</option>
                <option value="marukihigh">marukihigh</option>
                <option value="snp">snp</option>
            </param>
            <when value="marukilow">
                <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
            </when>
            <when value="marukihigh">
                <expand macro="variant_calling_options_vg"/>
            </when>
            <when value="snp">

            <conditional name="mode_cond">
                <param name="mode_select" value="denovo"/>
            </conditional>
            <param name="add_log" value="yes" />
            <param name="add_log_distribs" value="yes" />
            <output name="output_log" ftype="txt" file="gstacks/gstacks.log" lines_diff="8"/>
            <output name="distribs" ftype="txt" file="gstacks/gstacks.log.distribs" compare="sim_size"/>
            <output_collection name="gstacks_out" type="list" count="2">
                <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="2"/>
                <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz"/>
            </output_collection>

                    <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" />
                </conditional>
            </conditional>
            <param name="model_cond|model" value="snp"/>
            <param name="model_cond|gt_alpha" value="0.1" />
            <param name="model_cond|var_alpha" value="0.1" />
            <param name="add_log" value="yes" />
            <assert_command>
                <not_has_text text="-I bam_inputs" />
                <has_text text="-B " />
                <has_text text="--unpaired" />

must be consistent if repeated different files.
Otherwise read groups are unneeded and ignored.

**Output files**

- Assembled contigs and variant sites

- Optional outputs: Read alignments and log.distribs

@STACKS_INFOS@
]]>
    </help>
    <expand macro="citation" />