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annotate macros.xml @ 1:0de1b7cdad21 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 108e83ea251bee3b952cb49ef758e69294608c1d
author rnateam
date Wed, 02 Jan 2019 10:09:30 -0500
parents 159092b83639
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159092b83639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
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1 <macros>
1
0de1b7cdad21 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 108e83ea251bee3b952cb49ef758e69294608c1d
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2 <token name="@VERSION@">1.0.8</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@VERSION@">cmv</requirement>
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7 </requirements>
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8 </xml>
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9
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10 <xml name="stdio">
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11 <stdio>
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12 <exit_code range="1:" />
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13 </stdio>
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14 </xml>
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15
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16 <xml name="version">
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17 <version_command>
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18 <![CDATA[
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19 HMMV --version
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20 ]]>
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21 </version_command>
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22 </xml>
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23
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24 <xml name="common_parameters">
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25 <param name="alignment_filepath" type="data" format="stockholm" label="Input stockholm alignment" optional="true"/>
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26 <param name="output_format" type="select" label="Output format" help="pdf, svg, png, ps">
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27 <option value="pdf">pdf</option>
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28 <option value="svg">svg</option>
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29 <option value="png">png</option>
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30 <option value="ps">ps</option>
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31 </param>
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32 <param name="model_details" type="select" label="Specify visualization detail level." help="minimal,simple,detailed">
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33 <option value="minimal">minimal</option>
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34 <option value="simple">simple</option>
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35 <option value="detailed">detailed</option>
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36 </param>
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37 <param name="emission_layout" type="select" label="Specify layout of emission probabilites." help="score,probability,bar">
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38 <option value="score">score</option>
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39 <option value="probability">probability</option>
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40 <option value="bar">bar</option>
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41 </param>
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42 <param argument="-t" type="float" value="0.01" label="Transition probability threshold" help="Minimal value for a transition probability to be displayed (Default: 0.01)"/>
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43 <param argument="-c" type="float" value="2" label="Image scaling factor" help="Set uniform scaling factor for image size (Default: 2)"/>
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44 <param argument="-w" type="integer" value="100" label="Maximum image width" help="Set maximal width of result figure (Default: 100)" optional="true"/>
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45 <param argument="-n" type="integer" value="50" label="Stockholm alignment entries" help="Set cutoff for included stockholm alignment entries (Default: 50)" optional="true"/>
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46 </xml>
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47
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48 <xml name="vis_output">
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49 <collection name="output_pdfs" type="list" label="${tool.name} on ${on_string}: output.pdfs">
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50 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.pdf" format="pdf"/>
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51 <filter>common['output_format'] == 'pdf'</filter>
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52 </collection>
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53 <collection name="output_svg" type="list" label="${tool.name} on ${on_string}: output.svgs">
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54 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.svg" format="svg"/>
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55 <filter>common['output_format'] == 'svg'</filter>
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56 </collection>
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57 <collection name="output_png" type="list" label="${tool.name} on ${on_string}: output.pngs">
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58 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.png" format="png"/>
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59 <filter>common['output_format'] == 'png'</filter>
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60 </collection>
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61 <collection name="output_ps" type="list" label="${tool.name} on ${on_string}: output.ps">
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62 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.ps" format="ps"/>
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63 <filter>common['output_format'] == 'ps'</filter>
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64 </collection>
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65 </xml>
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66
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67 <token name="@COMMON_ARGS@">
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68 -d $common.model_details
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69 -e $common.emission_layout
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70 -n $common.n
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71 -w $common.w
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72 -c $common.c
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73 -t $common.t
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74 -f $common.output_format
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75 #if $common.alignment_filepath
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76 -s $common.alignment_filepath
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77 #end if
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78 </token>
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79
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80 <xml name="citations">
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81 <citations>
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82 <citation type="doi">10.1093/nar/gkt329</citation>
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83 </citations>
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84 </xml>
159092b83639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
85 </macros>
159092b83639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
86