comparison macros.xml @ 3:c207119ba5f6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"

2:fcce77c09289

            <requirement type="package" version="4.6.0">findutils</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@STACKS_VERSION@">2.53</token>
    <token name="@WRAPPER_VERSION@">0</token>
    <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 -->
    <token name="@PROFILE@">18.01</token>

    <xml name="citation">
        <citations>
            <citation type="doi">10.1111/mec.12354</citation>
            <citation type="doi">10.1111/mec.12330</citation>

        <option value="bfuCI">bfuCI</option>
        <option value="bgIII">bgIII</option>
        <option value="bsaHI">bsaHI</option>
        <option value="bspDI">bspDI</option>
        <option value="bstYI">bstYI</option>
        <option value="cac8I">cac8I</option>
        <option value="claI">claI</option>
        <option value="csp6I">csp6I</option>
        <option value="ddeI">ddeI</option>
        <option value="dpnII">dpnII</option>

        <option value="ecoT22I">ecoT22I</option>
        <option value="haeIII">haeIII</option>
        <option value="hindIII">hindIII</option>
        <option value="hinP1I">hinP1I</option>
        <option value="hpaII">hpaII</option>
        <option value="kpnI">kpnI</option>
        <option value="mluCI">mluCI</option>
        <option value="mseI">mseI</option>
        <option value="mslI">mslI</option>
        <option value="mspI">mspI</option>
        <option value="ncoI">ncoI</option>
        <option value="ndeI">ndeI</option>
        <option value="nheI">nheI</option>
        <option value="nlaIII">nlaIII</option>
        <option value="notI">notI</option>
        <option value="nsiI">nsiI</option>
        <option value="nspI">nspI</option>
        <option value="pstI">pstI</option>
        <option value="rsaI">rsaI</option>
        <option value="sacI">sacI</option>
        <option value="sau3AI">sau3AI</option>
        <option value="sbfI">sbfI</option>

    </xml>

    <xml name="populations_output_full">
        <expand macro="populations_output_light"/>

        <data format="txt" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.sql.tsv">
            <filter>genetic_map_options['map_type'] and genetic_map_options['map_format']</filter>
        </data>

        <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv-->
        <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv">
            <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
        </data>
        <data format="tabular" name="out_phistats_sum" label="${tool.name} on ${on_string} Summary of Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats_summary.tsv">
            <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
        </data>
        <data format="tabular" name="out_fststats_sum" label="${tool.name} on ${on_string} Summary of Fst statistics" from_work_dir="stacks_outputs/populations.fst_summary.tsv">
            <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
        </data>

        <!-- fasta_loci populations.loci.fa
             fasta_samples populations.samples.fa
             fasta_samples_raw populations.samples-raw.fa-->

        <!-- treemix populations.treemix -->
        <data format="tabular" name="out_treemix" label="${tool.name} on ${on_string} Treemix format" from_work_dir="stacks_outputs/populations.treemix">
            <filter>populations_output['treemix']</filter>
        </data>
    </xml>

    <!-- fastq output for kmer/clone-filter -->
    <xml name="fastq_output_filter">
        <data name="clean" format_source="fqinputs" label="${tool.name} on ${on_string}">
            <filter>input_type['input_type_select'] == 'single'</filter>
            <yield/>
        </data>
        <collection name="clean_pair" type="paired" format_source="fqinputs" label="${tool.name} on ${on_string}">
            <filter>input_type['input_type_select'] == 'paired'</filter>
            <yield/>
        </collection>
        <data name="discarded" format_source="fqinputs" label="${tool.name} on ${on_string}: discarded reads">
            <filter>capture and input_type['input_type_select'] == 'single'</filter>
            <yield/>
        </data>
        <collection name="discarded_pair" format_source="fqinputs" type="paired" label="${tool.name} on ${on_string}: discarded reads">
            <filter>capture and input_type['input_type_select'] == 'paired'</filter>
            <yield/>
        </collection>
    </xml>

3:c207119ba5f6

            <requirement type="package" version="4.6.0">findutils</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@STACKS_VERSION@">2.55</token>
    <token name="@WRAPPER_VERSION@">0</token>
    <token name="@PROFILE@">20.01</token>

    <xml name="citation">
        <citations>
            <citation type="doi">10.1111/mec.12354</citation>
            <citation type="doi">10.1111/mec.12330</citation>

        <option value="bfuCI">bfuCI</option>
        <option value="bgIII">bgIII</option>
        <option value="bsaHI">bsaHI</option>
        <option value="bspDI">bspDI</option>
        <option value="bstYI">bstYI</option>
        <option value="btgI">btgI</option>
        <option value="cac8I">cac8I</option>
        <option value="claI">claI</option>
        <option value="csp6I">csp6I</option>
        <option value="ddeI">ddeI</option>
        <option value="dpnII">dpnII</option>

        <option value="ecoT22I">ecoT22I</option>
        <option value="haeIII">haeIII</option>
        <option value="hindIII">hindIII</option>
        <option value="hinP1I">hinP1I</option>
        <option value="hpaII">hpaII</option>
        <option value="hpyCH4IV">hpyCH4IV</option>
        <option value="kpnI">kpnI</option>
        <option value="mluCI">mluCI</option>
        <option value="mseI">mseI</option>
        <option value="mslI">mslI</option>
        <option value="mspI">mspI</option>
        <option value="ncoI">ncoI</option>
        <option value="ndeI">ndeI</option>
        <option value="nheI">nheI</option>
        <option value="ngoMIV">ngoMIV</option>
        <option value="nlaIII">nlaIII</option>
        <option value="notI">notI</option>
        <option value="nsiI">nsiI</option>
        <option value="nspI">nspI</option>
        <option value="pacI">pacI</option>
        <option value="pspXI">pspXI</option>
        <option value="pstI">pstI</option>
        <option value="rsaI">rsaI</option>
        <option value="sacI">sacI</option>
        <option value="sau3AI">sau3AI</option>
        <option value="sbfI">sbfI</option>

    </xml>

    <xml name="populations_output_full">
        <expand macro="populations_output_light"/>

        <data format="txt" name="out_sql" label="${tool.name} on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.sql.tsv">
            <filter>genetic_map_options['map_type'] and genetic_map_options['map_format']</filter>
        </data>

        <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv-->
        <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv">
            <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter>
        </data>
        <data format="tabular" name="out_phistats_sum" label="${tool.name} on ${on_string} Summary of Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats_summary.tsv">
            <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter>
        </data>
        <data format="tabular" name="out_fststats_sum" label="${tool.name} on ${on_string} Summary of Fst statistics" from_work_dir="stacks_outputs/populations.fst_summary.tsv">
            <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter>
        </data>

        <!-- fasta_loci populations.loci.fa
             fasta_samples populations.samples.fa
             fasta_samples_raw populations.samples-raw.fa-->

        <!-- treemix populations.treemix -->
        <data format="tabular" name="out_treemix" label="${tool.name} on ${on_string} Treemix format" from_work_dir="stacks_outputs/populations.treemix">
            <filter>populations_output['treemix']</filter>
        </data>

        <!-- gtf populations.treemix -->
        <data format="gtf" name="out_gtf" label="${tool.name} on ${on_string} gtf" from_work_dir="stacks_outputs/populations.gtf">
            <filter>populations_output['gtf']</filter>
        </data>
    </xml>

    <!-- fastq output for kmer/clone-filter -->
    <xml name="fastq_output_filter" token_format="">
        <data name="clean" format="@FORMAT@" label="${tool.name} on ${on_string}">
            <filter>input_type['input_type_select'] == 'single'</filter>
            <yield/>
        </data>
        <collection name="clean_pair" type="paired" format="@FORMAT@" label="${tool.name} on ${on_string}">
            <filter>input_type['input_type_select'] == 'paired'</filter>
            <yield/>
        </collection>
        <data name="discarded" format="@FORMAT@" label="${tool.name} on ${on_string}: discarded reads">
            <filter>capture and input_type['input_type_select'] == 'single'</filter>
            <yield/>
        </data>
        <collection name="discarded_pair" format="@FORMAT@" type="paired" label="${tool.name} on ${on_string}: discarded reads">
            <filter>capture and input_type['input_type_select'] == 'paired'</filter>
            <yield/>
        </collection>
    </xml>