comparison macros.xml @ 4:7370bb65bad4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"

3:eb784fa07f80

            <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>

        <expand macro="gstacks_outputs_macro"/>
        <data format="txt" name="distribs" label="${tool.name} on ${on_string} log.distribs" from_work_dir="stacks_outputs/gstacks.log.distribs">
            <filter>add_log_distribs</filter>
        </data>
        <collection name="gstacks_alns_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Read alignments">
            <discover_datasets pattern="(?P&lt;name&gt;.*).alns.bam$" ext="bam" directory="stacks_outputs"/>
            <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap!=None</filter>
        </collection>
        <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam">
            <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap==None</filter>
        </data>
    </xml>
    <xml name="gstacks_outputs_macro" token_tooladd="">
        <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites">
            <discover_datasets pattern="(?P&lt;name&gt;catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs"/>

4:7370bb65bad4

            <yield/>
        </requirements>
    </xml>

    <token name="@STACKS_VERSION@">2.55</token>
    <token name="@WRAPPER_VERSION@">1</token>
    <token name="@PROFILE@">20.05</token>

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

        <expand macro="gstacks_outputs_macro"/>
        <data format="txt" name="distribs" label="${tool.name} on ${on_string} log.distribs" from_work_dir="stacks_outputs/gstacks.log.distribs">
            <filter>add_log_distribs</filter>
        </data>
        <collection name="gstacks_alns_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Read alignments">
            <discover_datasets pattern="(?P&lt;name&gt;.*).alns.bam$" format="bam" directory="stacks_outputs"/>
            <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] and popmap!=None</filter>
        </collection>
        <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam">
            <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] and popmap==None</filter>
        </data>
    </xml>
    <xml name="gstacks_outputs_macro" token_tooladd="">
        <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites">
            <discover_datasets pattern="(?P&lt;name&gt;catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs"/>