comparison flash.xml @ 6:01a4ebf1f237 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 7e92326c8481e440066c4aabb13d373dec570e2e

5:a27654fc4270

<?xml version="1.0"?>
<tool id="flash" name="FLASH" version="@VERSION@.4">
    <description>adjust length of short reads</description>
    <macros>
        <token name="@VERSION@">1.2.11</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">flash</requirement>

        <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)">
            <filter>allow_outies and generate_histogram</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="select_layout" value="individual" />
            <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" />
            <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" />
            <param name="generate_histogram" value="false" />
            <param name="save_log" value="true" />
            <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" />
            <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" />
            <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" />
            <output name="hist" file="flash_hist_out1.tabular" />
            <output name="log">
              <assert_contents>
                <has_line_matching expression=".*Percent combined: 3.60%" />
              </assert_contents>
            </output>
        </test>
        <test>
            <param name="select_layout" value="individual" />
            <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" />
            <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" />
            <param name="allow_outies" value="true" />
            <param name="generate_histogram" value="true" />
            <param name="save_log" value="true" />            
            <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" />
            <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" />
            <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" />
            <output name="hist" file="flash_hist_out2.tabular" />
            <output name="histogram" file="flash_hist_out2.txt" />
            <output name="hist_in" file="flash_hist_in_out2.tabular" />
            <output name="histogram_in" file="flash_hist_in_out2.txt" />
            <output name="hist_out" file="flash_hist_out_out2.tabular" />

              <assert_contents>
                <has_line_matching expression=".*Percent combined: 3.80%" />
              </assert_contents>
            </output>
        </test>
        <test>
            <param name="select_layout" value="collection" />
            <param name="generate_histogram" value="false" />
            <param name="reads">
                <collection type="paired">
                    <element name="forward" value="flash_forward_in3.fastqillumina" ftype="fastqillumina" />
                    <element name="reverse" value="flash_reverse_in3.fastqillumina" ftype="fastqillumina" />
                </collection>
            </param>
            <output name="merged_reads" file="flash_merged_out3.fastqillumina" ftype="fastqillumina" />
            <output name="unmerged_reads_f" file="flash_unmerged_f_out3.fastqillumina" ftype="fastqillumina" />
            <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" />
            <output name="hist" file="flash_hist_out3.tabular" />
        </test>
        <test>
            <param name="select_layout" value="individual" />
            <param name="forward" value="flash_forward_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
            <param name="reverse" value="flash_reverse_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
            <param name="generate_histogram" value="false" />
            <param name="save_log" value="true" />

              <assert_contents>
                <has_line_matching expression=".*Percent combined: 3.60%" />
              </assert_contents>
            </output>
        </test>
        <test>
            <param name="select_layout" value="collection" />
            <param name="generate_histogram" value="false" />
            <param name="reads">
                <collection type="paired">
                    <element name="forward" value="flash_forward_in5.fastqsanger.gz" ftype="fastqsanger.gz" />

6:01a4ebf1f237

<tool id="flash" name="FLASH" version="@VERSION@.4" profile="21.05">
    <description>adjust length of short reads</description>
    <xrefs>
        <xref type="bio.tools">flash</xref>
    </xrefs>
    <macros>
        <token name="@VERSION@">1.2.11</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">flash</requirement>

        <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)">
            <filter>allow_outies and generate_histogram</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="5">
            <param name="select_layout" value="individual" />
            <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" />
            <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" />
            <param name="generate_histogram" value="false" />
            <param name="save_log" value="true" />
            <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" sort="true" />
            <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" sort="true" />
            <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" sort="true" />
            <output name="hist" file="flash_hist_out1.tabular" />
            <output name="log">
              <assert_contents>
                <has_line_matching expression=".*Percent combined: 3.60%" />
              </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="10">
            <param name="select_layout" value="individual" />
            <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" />
            <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" />
            <param name="allow_outies" value="true" />
            <param name="generate_histogram" value="true" />
            <param name="save_log" value="true" />            
            <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" sort="true" />
            <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" sort="true" />
            <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" sort="true" />
            <output name="hist" file="flash_hist_out2.tabular" />
            <output name="histogram" file="flash_hist_out2.txt" />
            <output name="hist_in" file="flash_hist_in_out2.tabular" />
            <output name="histogram_in" file="flash_hist_in_out2.txt" />
            <output name="hist_out" file="flash_hist_out_out2.tabular" />

              <assert_contents>
                <has_line_matching expression=".*Percent combined: 3.80%" />
              </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <param name="select_layout" value="collection" />
            <param name="generate_histogram" value="false" />
            <param name="reads">
                <collection type="paired">
                    <element name="forward" value="flash_forward_in3.fastqillumina" ftype="fastqillumina" />
                    <element name="reverse" value="flash_reverse_in3.fastqillumina" ftype="fastqillumina" />
                </collection>
            </param>
            <output name="merged_reads" file="flash_merged_out3.fastqillumina" ftype="fastqillumina" sort="true" />
            <output name="unmerged_reads_f" file="flash_unmerged_f_out3.fastqillumina" ftype="fastqillumina" sort="true" />
            <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" sort="true" />
            <output name="hist" file="flash_hist_out3.tabular" />
        </test>
        <test expect_num_outputs="5">
            <param name="select_layout" value="individual" />
            <param name="forward" value="flash_forward_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
            <param name="reverse" value="flash_reverse_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
            <param name="generate_histogram" value="false" />
            <param name="save_log" value="true" />

              <assert_contents>
                <has_line_matching expression=".*Percent combined: 3.60%" />
              </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <param name="select_layout" value="collection" />
            <param name="generate_histogram" value="false" />
            <param name="reads">
                <collection type="paired">
                    <element name="forward" value="flash_forward_in5.fastqsanger.gz" ftype="fastqsanger.gz" />