comparison unicycler.xml @ 11:8f9f06995f98 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc

10:d10bdad2fd17

<description>pipeline for bacterial genomes</description>
    <macros>
        <token name="@TOOL_VERSION@">0.5.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">unicycler</xref>
    </xrefs>
    <edam_topics>
        <edam_topic>topic_0196</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_0525</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">unicycler</requirement>
        <requirement type="package" version="1.15.1">samtools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
## Preparing files
#set $uncompressed = ('fastqsanger','fastq')
#set $compressed = ('fastqsanger.gz','fastq.gz')
#if str( $paired_unpaired.fastq_input_selector ) == "paired"
    #if $paired_unpaired.fastq_input1.file_ext in $uncompressed

        <param argument="--keep" type="select" label="Outputs to keep" help="Level of file retention. Default: 1">
            <option value="0">0: only keep final files</option>
            <option value="1" selected="true">1: save graphs at main checkpoints</option>
            <option value="2">2: also keep SAM</option>
        </param>
    </inputs>
    <outputs>
        <data name="assembly_graph" format="gfa1" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
        <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/>
        <collection name="spades_collection" type="list" label="${tool.name} on ${on_string}: SPAdes graphs">
            <discover_datasets pattern="__designation_and_ext__" format="gfa1" directory="spades_graphs"/>
            <filter>keep != "0"</filter>
        </collection>
        <data name="bam_file" format="bam" from_work_dir="read_alignment/long_read_alignments.bam" label="${tool.name} on ${on_string}: Long read alignments BAM">
            <filter>keep == "2" and long</filter>
        </data>

                <assert_contents>
                    <has_text text=">1" />
                </assert_contents>
            </output>
        </test>
        <!-- Test keep value = 1 -->
        <test expect_num_outputs="3">
            <conditional name="paired_unpaired">
                <param name="fastq_input_selector" value="paired" />
                <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />

                <element name="001_spades_graph_k027">
                    <assert_contents>
                        <has_text text="TTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAAC"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output name="bam_file" ftype="bam">
                <assert_contents>
                    <has_size value="2084" delta="100"/>
                </assert_contents>

11:8f9f06995f98

<description>pipeline for bacterial genomes</description>
    <macros>
        <token name="@TOOL_VERSION@">0.5.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <edam_topics>
        <edam_topic>topic_0196</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_0525</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">unicycler</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">unicycler</requirement>
        <requirement type="package" version="1.15.1">samtools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#for r in $reuse
    ln -s $r.reuse_file ${r.reuse_step}.gfa &&
#end for

## Preparing files
#set $uncompressed = ('fastqsanger','fastq')
#set $compressed = ('fastqsanger.gz','fastq.gz')
#if str( $paired_unpaired.fastq_input_selector ) == "paired"
    #if $paired_unpaired.fastq_input1.file_ext in $uncompressed

        <param argument="--keep" type="select" label="Outputs to keep" help="Level of file retention. Default: 1">
            <option value="0">0: only keep final files</option>
            <option value="1" selected="true">1: save graphs at main checkpoints</option>
            <option value="2">2: also keep SAM</option>
        </param>
        <repeat name="reuse" title="Reuse checkpoint files from earlier runs" max="1" help="">
            <param name="reuse_file" type="data" optional="false" format="gfa1" label="Checkpoint file"/>
            <param name="reuse_step" type="select" label="Checkpoint">
                <option value="002_depth_filter">002_depth_filter</option>
                <option value="003_overlaps_removed">003_overlaps_removed</option>
                <option value="004_bridges_applied">004_bridges_applied</option>
            </param>
        </repeat>
    </inputs>
    <outputs>
        <data name="assembly_graph" format="gfa1" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
        <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/>
        <collection name="spades_collection" type="list" label="${tool.name} on ${on_string}: SPAdes graphs">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gfa" format="gfa1" directory="spades_graphs"/>
            <filter>keep != "0"</filter>
        </collection>
        <data name="bam_file" format="bam" from_work_dir="read_alignment/long_read_alignments.bam" label="${tool.name} on ${on_string}: Long read alignments BAM">
            <filter>keep == "2" and long</filter>
        </data>

                <assert_contents>
                    <has_text text=">1" />
                </assert_contents>
            </output>
        </test>
        <!-- test checkpoint graph reuse 
             TODO more precise test and check difference to call wo reuse -->
        <test expect_num_outputs="2">
            <conditional name="paired_unpaired">
                <param name="fastq_input_selector" value="paired_collection"/>
                <param name="fastq_input1">
                    <collection type="paired">
                        <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" />
                        <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" />
                    </collection>
                </param>
            </conditional>
            <param name="long" value="only_long.fasta" ftype="fasta" />
            <repeat name="reuse">
                <param name="reuse_file" value="phix__spades_graph.gfa1"/>
                <param name="reuse_step" value="002_depth_filter"/>
            </repeat>
            <param name="keep" value="0"/>
            <output name="assembly_graph" ftype="gfa1">
                <assert_contents>
                    <has_text text="S" />
                </assert_contents>
            </output>
            <output name="assembly" ftype="fasta">
                <assert_contents>
                    <has_text text=">1" />
                </assert_contents>
            </output>
        </test>
        <!-- Test keep value = 1 -->
        <test expect_num_outputs="3">
            <conditional name="paired_unpaired">
                <param name="fastq_input_selector" value="paired" />
                <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />

                <element name="001_spades_graph_k027">
                    <assert_contents>
                        <has_text text="TTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAAC"/>
                    </assert_contents>
                </element>
                <!-- there are gfa files for more k that are not tested explicily
                     Aim of testing these is to be sure about the names of the graphs,
                     since they are used for reuse. Hence if there is a change here
                     update reuse accordingly-->
                <element name="001_spades_graph_k127">
                    <assert_contents>
                        <has_line_matching expression="^S.*"/>
                    </assert_contents>
                </element>
                <element name="002_depth_filter">
                    <assert_contents>
                        <has_line_matching expression="^S.*"/>
                    </assert_contents>
                </element>
                <element name="003_overlaps_removed">
                    <assert_contents>
                        <has_line_matching expression="^S.*"/>
                    </assert_contents>
                </element>
                <element name="004_bridges_applied">
                    <assert_contents>
                        <has_line_matching expression="^S.*"/>
                    </assert_contents>
                </element>
                <element name="005_final_clean">
                    <assert_contents>
                        <has_line_matching expression="^S.*"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output name="bam_file" ftype="bam">
                <assert_contents>
                    <has_size value="2084" delta="100"/>
                </assert_contents>