comparison diamond.xml @ 41:b5a8cc7a993f draft

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40:ae2a362dd513

<tool id="bg_diamond" name="Diamond" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
    <description>alignment tool for short sequences against a protein database</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <xrefs>
        <xref type="bio.tools">diamond</xref>
    </xrefs>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command detect_errors="aggressive">
<![CDATA[

        ln -s ${ref_db_source.index.fields.db_path} ./database.dmnd
    #end if

    &&

    diamond
        $method_cond.method_select
        --quiet
        --threads "\${GALAXY_SLOTS:-12}"
        --db ./database
        --query '$query'

                <option value="indexed">Use a built-in index</option>
                <option value="history">Use one from the history</option>
            </param>
            <when value="indexed">
                <param name="index" type="select" label="Select a reference database" help="If your database of interest is not listed, contact your Galaxy admin">
                    <options from_data_table="diamond_database">
                        <filter type="sort_by" column="2"/>
                        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                    </options>
                </param>
            </when>

        </data>
        <data format_source="query" name="alqueries" label="${tool.name} on ${on_string}: aligned queries">
            <filter>output_section['output_unal'] and "--un" in output_section['output_unal']</filter>
        </data>
    </outputs>
    <tests>
        <!--Test 01-->
        <test expect_num_outputs="3">
            <conditional name="method_cond">
                <param name="method_select" value="blastp" />
            </conditional>
            <param name="query" value="protein.fasta" ftype="fasta"/>
            <conditional name="ref_db_source">
                <param name="db_source" value="history"/>
                <param name="reference_database" value="db-wtax.dmnd"/>
            </conditional>
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="6"/>
                    <!-- removed ,cigar from test: https://github.com/bbuchfink/diamond/issues/532 -->
                    <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,scovhsp,sskingdoms,skingdoms,sphylums"/>
                    <param name="unal" value="true"/>
                </conditional>
            </section>
            <conditional name="sens_cond">
                <param name="sensitivity" value=""/>
            </conditional>
            <param name="matrix" value="BLOSUM62"/>
            <param name="comp_based_stats" value="1"/>
            <param name="masking" value="1"/>
            <conditional name="hit_filter">
                <param name="hit_filter_select" value="max"/>
                <param name="max_target_seqs" value="25" />
            </conditional>
            <conditional name="filter_score">
                <param name="filter_score_select" value="evalue"/>
                <param name="evalue" value="0.001" />
            </conditional>
            <param name="id" value="0"/>
            <param name="query_cover" value="0"/>
            <conditional name="sens_cond">
                <param name="block_size" value="2"/>
            </conditional>
            <param name="output_unal" value="--al,--un"/>
            <output name="unalqueries">
                <assert_contents>
                    <has_line line=">shuffled sequence that should go to unaligned"/>
                </assert_contents>
            </output>
            <output name="alqueries">
                <assert_contents>
                    <has_line line=">sequence more text"/>
                </assert_contents>
            </output>
            <output name="blast_tabular" file="diamond_results.tabular"/>
        </test>
        <!--Test 02-->
        <test expect_num_outputs="1">
            <conditional name="method_cond">
                <param name="method_select" value="blastp" />
            </conditional>
            <param name="query" value="protein.fasta" ftype="fasta"/>
            <conditional name="ref_db_source">
                <param name="db_source" value="history"/>
                <param name="reference_database" value="db-wtax.dmnd"/>
            </conditional>
            <conditional name="tax_cond">
                <param name="tax_select" value="list"/>
                <param name="taxonlist" value="2" />
            </conditional>
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="6"/>
                    <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
                </conditional>
            </section>
            <conditional name="sens_cond">
                <param name="sensitivity" value=""/>
            </conditional>
            <param name="matrix" value="BLOSUM62"/>
            <param name="comp_based_stats" value="1"/>
            <param name="masking" value="1"/>
            <conditional name="hit_filter">
                <param name="hit_filter_select" value="max"/>
                <param name="max_target_seqs" value="25" />
            </conditional>
            <conditional name="filter_score">
                <param name="filter_score_select" value="evalue"/>
                <param name="evalue" value="0.001" />
            </conditional>
            <param name="id" value="0"/>
            <param name="query_cover" value="0"/>
            <conditional name="sens_cond">
                <param name="block_size" value="2"/>
            </conditional>
            <output name="blast_tabular" file="diamond_results.wtax.tabular"/>
        </test>
        <!--Test 03-->
        <test expect_num_outputs="1">
            <conditional name="method_cond">
                <param name="method_select" value="blastx" />
                <conditional name="frameshift_cond">
                    <param name="frameshift_select" value="yes"/>
                </conditional>
            </conditional>
            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
            <conditional name="ref_db_source">
                <param name="db_source" value="history"/>
                <param name="reference_database" value="db.dmnd"/>
            </conditional>
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="0"/>
                </conditional>
            </section>
            <conditional name="sens_cond">
                <param name="sensitivity" value=""/>
            </conditional>
            <param name="matrix" value="BLOSUM62"/>
            <param name="comp_based_stats" value="1"/>
            <param name="masking" value="1"/>
            <conditional name="hit_filter">
                <param name="hit_filter_select" value="top"/>
                <param name="top" value="10" />
            </conditional>
            <conditional name="filter_score">
                <param name="filter_score_select" value="min-score"/>
                <param name="min_score" value="1" />
            </conditional>
            <param name="id" value="0"/>
            <param name="query_cover" value="0"/>
            <conditional name="sens_cond">
                <param name="block_size" value="2"/>
            </conditional>
            <output name="blast_tabular" file="diamond_results.pairwise"/>
        </test>
        <!--Test 04-->
        <test expect_num_outputs="1">
            <conditional name="method_cond">
                <param name="method_select" value="blastp" />
            </conditional>
            <param name="query" value="protein.fasta" ftype="fasta"/>
            <conditional name="ref_db_source">
                <param name="db_source" value="history"/>
                <param name="reference_database" value="db-wtax.dmnd"/>
            </conditional>
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="100"/>
                    <param name="salltitles" value="false"/>
                    <param name="sallseqid" value="false"/>
                </conditional>
            </section>
            <output name="daa_output" file="diamond_results.daa" compare="sim_size" delta="10"/>
        </test>
        <!--Test 05-->
        <test expect_num_outputs="1">
            <conditional name="method_cond">
                <param name="method_select" value="blastx" />
                <conditional name="frameshift_cond">
                    <param name="frameshift_select" value="yes"/>
                </conditional>
            </conditional>
            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
            <conditional name="ref_db_source">
                <param name="db_source" value="indexed"/>
                <param name="index" value="testDb"/>
            </conditional>
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="0"/>
                </conditional>
            </section>
            <conditional name="sens_cond">
                <param name="sensitivity" value=""/>
            </conditional>
            <param name="matrix" value="BLOSUM62"/>
            <param name="comp_based_stats" value="1"/>
            <param name="masking" value="1"/>
            <conditional name="hit_filter">
                <param name="hit_filter_select" value="top"/>
                <param name="top" value="10" />
            </conditional>
            <conditional name="filter_score">
                <param name="filter_score_select" value="min-score"/>
                <param name="min_score" value="1" />
            </conditional>
            <param name="id" value="0"/>
            <param name="query_cover" value="0"/>
            <conditional name="sens_cond">
                <param name="block_size" value="2"/>
            </conditional>
            <output name="blast_tabular" file="diamond_results.pairwise"/>
        </test>
        <!-- Test 06 iterate option-->
        <test expect_num_outputs="1">
            <conditional name="method_cond">
                <param name="method_select" value="blastx" />
            </conditional>
            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
            <conditional name="ref_db_source">
                <param name="db_source" value="indexed"/>
                <param name="index" value="testDb"/>
            </conditional>
            <param name="iterate" value="true"/>
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="6"/>
                    <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
                </conditional>
            </section>
            <output name="blast_tabular" file="diamond_results_iterate.tabular"/>
        </test>
        <!--Test 07 algo option-->
        <test expect_num_outputs="1">
            <conditional name="method_cond">
                <param name="method_select" value="blastx" />
            </conditional>
            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
            <conditional name="ref_db_source">
                <param name="db_source" value="indexed"/>
                <param name="index" value="testDb"/>
            </conditional>
            <param name="algo" value="1"/>
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="6"/>
                    <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
                </conditional>
            </section>
            <output name="blast_tabular" file="diamond_results_algorithm.tabular"/>
        </test>
        <!--Test 08 global-ranking option-->
        <test expect_num_outputs="1">
            <conditional name="method_cond">
                <param name="method_select" value="blastx" />
            </conditional>
            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
            <conditional name="ref_db_source">
                <param name="db_source" value="indexed"/>
                <param name="index" value="testDb"/>
            </conditional>
            <param name="global_ranking" value="10"/>
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="6"/>
                    <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
                </conditional>
            </section>
            <output name="blast_tabular" file="diamond_results_global_ranking.tabular"/>
        </test>
        <!--Test 09 max-hsps option-->
        <test expect_num_outputs="1">
            <conditional name="method_cond">
                <param name="method_select" value="blastx" />
            </conditional>
            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
            <conditional name="ref_db_source">
                <param name="db_source" value="indexed"/>
                <param name="index" value="testDb"/>
            </conditional>
            <param name="max_hsps" value="10"/>
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="6"/>
                    <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
                </conditional>
            </section>
            <output name="blast_tabular" file="diamond_results_max_hsps.tabular"/>
        </test>
        <!--Test 10 seed-cut option-->
        <test expect_num_outputs="1">
            <conditional name="method_cond">
                <param name="method_select" value="blastx" />
            </conditional>
            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
            <conditional name="ref_db_source">
                <param name="db_source" value="indexed"/>
                <param name="index" value="testDb"/>
            </conditional>
            <param name="seed_cut" value="100"/>
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="6"/>
                    <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
                </conditional>
            </section>
            <output name="blast_tabular" file="diamond_results_seed_cut.tabular"/>
        </test>
        <!--Test 11 freq-masking option-->
        <test expect_num_outputs="1">
            <conditional name="method_cond">
                <param name="method_select" value="blastx" />
            </conditional>
            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
            <conditional name="ref_db_source">
                <param name="db_source" value="indexed"/>
                <param name="index" value="testDb"/>
            </conditional>
            <param name="freq_masking" value="true"/>
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="6"/>
                    <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
                </conditional>
            </section>
            <output name="blast_tabular" file="diamond_results_freq_masking.tabular"/>
        </test>
        <!--Test 12 motif-masking option-->
        <test expect_num_outputs="1">
            <conditional name="method_cond">
                <param name="method_select" value="blastx" />
            </conditional>
            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
            <conditional name="ref_db_source">
                <param name="db_source" value="indexed"/>
                <param name="index" value="testDb"/>
            </conditional>
            <section name="advanced_section">
                <param name="motif_masking" value="1"/>
            </section>
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="6"/>
                    <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
                </conditional>
            </section>
            <output name="blast_tabular" file="diamond_results_motif_masking.tabular"/>
        </test>
    </tests>
    <help>
<![CDATA[

**What it does**

41:b5a8cc7a993f

<tool id="pl_diamond" name="PL_Diamond" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
    <description>alignment tool for short sequences against a protein database</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command detect_errors="aggressive">
<![CDATA[

        ln -s ${ref_db_source.index.fields.db_path} ./database.dmnd
    #end if

    &&

    /usr/bin/diamond
        $method_cond.method_select
        --quiet
        --threads "\${GALAXY_SLOTS:-12}"
        --db ./database
        --query '$query'

                <option value="indexed">Use a built-in index</option>
                <option value="history">Use one from the history</option>
            </param>
            <when value="indexed">
                <param name="index" type="select" label="Select a reference database" help="If your database of interest is not listed, contact your Galaxy admin">
                    <options from_data_table="pl_diamond_database">
                        <filter type="sort_by" column="2"/>
                        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                    </options>
                </param>
            </when>

        </data>
        <data format_source="query" name="alqueries" label="${tool.name} on ${on_string}: aligned queries">
            <filter>output_section['output_unal'] and "--un" in output_section['output_unal']</filter>
        </data>
    </outputs>
    <help>
<![CDATA[

**What it does**