comparison bcftools_plugin_mendelian.xml @ 5:f0747a281247 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e

4:31f2ab4d1cac

    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
@PREPARE_INPUT_FILE@
#set $section = $sec_restrict
@PREPARE_TARGETS_FILE@

bcftools plugin @EXECUTABLE@

## VCF input section
#set $section = $sec_restrict

 #if 'x' in $modes:
  --list x
 #end if
#end if
2> tmp_stderr
> "$output_file"
&& cat tmp_stderr
]]>
</command>
    <inputs>
        <expand macro="macro_input" />

                </when>
            </conditional>
            <param name="mode" type="select" label="Action" multiple="true" min="1">
                <option value="count">count the number of consistent sites</option>
                <option value="delete">delete inconsistent genotypes (set to './.')</option>
                <option value="+">consistent sites (+)</option>
                <option value="x">inconsistent sites (x)</option>
            </param>
        </section>
        <expand macro="macro_select_output_type" />
    </inputs>
    <outputs>

            <param name="child" value="NA00006" />
            <param name="mode" value="delete" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="2698758" />
                    <not_has_text text="2698769" />
                </assert_contents>
            </output>
        </test>
        <test>
            <!-- This is just a test on a random file, should have a real test case -->

            <param name="child" value="NA00006" />
            <param name="mode" value="x" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <not_has_text text="2698758" />
                    <has_text text="2698769" />
                </assert_contents>
            </output>
        </test>

5:f0747a281247

    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
@PREPARE_INPUT_FILE@
#set $section = $sec_restrict
@PREPARE_TARGETS_FILE@
@PREPARE_REGIONS_FILE@

bcftools plugin @EXECUTABLE@

## VCF input section
#set $section = $sec_restrict

 #if 'x' in $modes:
  --list x
 #end if
#end if
2> tmp_stderr
> '$output_file'
&& cat tmp_stderr
]]>
</command>
    <inputs>
        <expand macro="macro_input" />

                </when>
            </conditional>
            <param name="mode" type="select" label="Action" multiple="true" min="1">
                <option value="count">count the number of consistent sites</option>
                <option value="delete">delete inconsistent genotypes (set to './.')</option>
                <option value="+">list consistent sites (+)</option>
                <option value="x">list inconsistent sites (x)</option>
            </param>
        </section>
        <expand macro="macro_select_output_type" />
    </inputs>
    <outputs>

            <param name="child" value="NA00006" />
            <param name="mode" value="delete" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="mendelian" />
                    <has_text_matching expression="X\t2698769\t.\tAAG\tA\t999\t.\t.\tGT:PL:GP\t./."/>
                </assert_contents>
            </output>
        </test>
        <test>
            <!-- This is just a test on a random file, should have a real test case -->

            <param name="child" value="NA00006" />
            <param name="mode" value="x" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="mendelian" />
                    <not_has_text text="2698758" />
                    <has_text text="2698769" />
                </assert_contents>
            </output>
        </test>