comparison stacks_refmap.xml @ 1:a8d93e132d3b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty

0:bd0bf17caa4d

$paired_select
-o stacks_outputs
-T \${GALAXY_SLOTS:-1}
--var-alpha $model_options.var_alpha
--gt-alpha $model_options.gt_alpha
    ]]></command>

    <inputs>
        <expand macro="bam_input_macro"/>
        <param argument="--popmap" type="data" format="tabular,txt" label="Population map" />

                    <element name="PopA_02" ftype="bam" value="refmap/PopA_01.bam" />
               </collection>
            </param>
            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
            <param name="add_log" value="yes" />
            <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
            <!-- TODO test for outputs -->
        </test>
        <test>
            <param name="input_type|input_type_selector" value="manual"/>
            <param name="input_type|input_bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>

                <has_text text="--unpaired" />
                <has_text text="--var-alpha 0.1" />
                <has_text text="--gt-alpha 0.1" />
            </assert_command>
            <param name="add_log" value="yes" />
            <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
        </test>
    </tests>

    <help>
<![CDATA[

1:a8d93e132d3b

$paired_select
-o stacks_outputs
-T \${GALAXY_SLOTS:-1}
--var-alpha $model_options.var_alpha
--gt-alpha $model_options.gt_alpha

&& mv stacks_outputs/ref_map.log $output_log
    ]]></command>

    <inputs>
        <expand macro="bam_input_macro"/>
        <param argument="--popmap" type="data" format="tabular,txt" label="Population map" />

                    <element name="PopA_02" ftype="bam" value="refmap/PopA_01.bam" />
               </collection>
            </param>
            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
            <param name="add_log" value="yes" />
            <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
            <!-- TODO test for outputs -->
        </test>
        <test>
            <param name="input_type|input_type_selector" value="manual"/>
            <param name="input_type|input_bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>

                <has_text text="--unpaired" />
                <has_text text="--var-alpha 0.1" />
                <has_text text="--gt-alpha 0.1" />
            </assert_command>
            <param name="add_log" value="yes" />
            <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
        </test>
    </tests>

    <help>
<![CDATA[