annotate hisat2_macros.xml @ 24:61ee47027bd3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 67cc9b86dcb40c7691cc85b77428117be25d6046
author iuc
date Thu, 15 Nov 2018 10:31:25 -0500
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1 <macros>
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2 <xml name="paired_end_options">
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4 <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand information"
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5 help="'FR' means a read corresponds to a transcript. 'RF' means a read corresponds to the reverse complemented counterpart of a transcript. With this option being used, every read alignment will have an XS attribute tag: '+' means a read belongs to a transcript on '+' strand of genome. '-' means a read belongs to a transcript on '-' strand of genome.">
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6 <option value="">Unstranded</option>
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7 <option value="FR">Forward (FR)</option>
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8 <option value="RF">Reverse (RF)</option>
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9 </param>
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11 <conditional name="paired_options">
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12 <param name="paired_options_selector" type="select" label="Paired-end options" help="See &quot;Alignment Options&quot; section of Help below for information">
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13 <option value="defaults">Use default values</option>
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14 <option value="advanced">Specify paired-end parameters</option>
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15 </param>
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16 <when value="defaults"/>
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17 <when value="advanced">
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18 <param name="fr_rf_ff" argument="--fr/--rf/--ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand"
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19 help="E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)">
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20 <option value="--fr" selected="True">--fr</option>
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21 <option value="--rf">--rf</option>
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22 <option value="--ff">--ff</option>
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23 </param>
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24 <param argument="--no-mixed" name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="By default, when `hisat2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default: False"/>
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25 <param argument="--no-discordant" name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `hisat2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default: False"/>
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26 </when>
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27 </conditional>
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29 </xml>
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31 <xml name="dbKeyActions">
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32 <actions>
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33 <conditional name="reference_genome.source">
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34 <when value="indexed">
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35 <action type="metadata" name="dbkey">
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36 <option type="from_data_table" name="hisat2_indexes" column="1">
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37 <filter type="param_value" ref="reference_genome.index" column="0"/>
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38 </option>
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39 </action>
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40 </when>
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41 <when value="history">
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42 <action type="metadata" name="dbkey">
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43 <option type="from_param" name="reference_genome.history_item" param_attribute="dbkey" />
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44 </action>
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45 </when>
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46 </conditional>
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47 </actions>
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48 </xml>
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49
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50 </macros>