Mercurial > repos > nasuno > tophat2_aurora

annotate tophat_macros.xml @ 0:589de4bdaca4 default tip

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for Apache Aurora jobrunner
author Makoto Nasuno <nasuno@ascade.co.jp>
date Fri, 26 Feb 2016 14:23:22 +0900
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589de4bdaca4 for Apache Aurora jobrunner
Makoto Nasuno <nasuno@ascade.co.jp>
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1 <macros>
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2 <macro name="refGenomeSourceConditional">
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3 <conditional name="refGenomeSource">
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4 <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options">
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5 <option value="indexed" selected="True">Use a built-in genome</option>
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6 <option value="history">Use a genome from history</option>
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7 </param>
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8 <when value="indexed">
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9 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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10 <yield />
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11 </param>
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12 </when>
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13 <when value="history">
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14 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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15 </when> <!-- history -->
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16 </conditional> <!-- refGenomeSource -->
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17 </macro>
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18 <macro name="indel_searchConditional">
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19 <conditional name="indel_search">
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20 <param name="allow_indel_search" type="select" label="Allow indel search">
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21 <option value="Yes">Yes</option>
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22 <option value="No">No</option>
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23 </param>
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24 <when value="No"/>
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25 <when value="Yes">
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26 <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
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27 <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
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28 </when>
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29 </conditional>
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30 </macro>
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31 <macro name="own_junctionsConditional">
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32 <conditional name="own_junctions">
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33 <param name="use_junctions" type="select" label="Use Own Junctions">
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34 <option value="No">No</option>
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35 <option value="Yes">Yes</option>
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36 </param>
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37 <when value="Yes">
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38 <conditional name="gene_model_ann">
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39 <param name="use_annotations" type="select" label="Use Gene Annotation Model">
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40 <option value="No">No</option>
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41 <option value="Yes">Yes</option>
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42 </param>
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43 <when value="No" />
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44 <when value="Yes">
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45 <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
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46 </when>
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47 </conditional>
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48 <expand macro="raw_juncsConditional" />
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49 <expand macro="no_novel_juncsParam" />
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50 </when>
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51 <when value="No" />
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52 </conditional> <!-- /own_junctions -->
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53 </macro>
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54 <macro name="raw_juncsConditional">
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55 <conditional name="raw_juncs">
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56 <param name="use_juncs" type="select" label="Use Raw Junctions">
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57 <option value="No">No</option>
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58 <option value="Yes">Yes</option>
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59 </param>
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60 <when value="No" />
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61 <when value="Yes">
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62 <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
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63 </when>
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64 </conditional>
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65 </macro>
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66 <macro name="no_novel_juncsParam">
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67 <param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
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68 <option value="No">No</option>
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69 <option value="Yes">Yes</option>
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70 </param>
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71 </macro>
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72 </macros>