Mercurial > repos > iuc > trinity
comparison macros.xml @ 32:77cf519a812e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
| author | iuc |
|---|---|
| date | Tue, 11 Apr 2023 19:57:45 +0000 |
| parents | 48636f857c4b |
| children |
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| 31:d2bc35f3d1c5 | 32:77cf519a812e |
|---|---|
| 1 <?xml version="1.0"?> | |
| 2 <macros> | 1 <macros> |
| 3 <xml name="requirements"> | 2 <xml name="requirements"> |
| 4 <requirements> | 3 <requirements> |
| 5 <requirement type="package" version="@WRAPPER_VERSION@">trinity</requirement> | 4 <requirement type="package" version="@TOOL_VERSION@">trinity</requirement> |
| 6 <yield/> | 5 <yield/> |
| 7 </requirements> | 6 </requirements> |
| 8 </xml> | 7 </xml> |
| 9 <xml name="bio_tools"> | 8 <xml name="bio_tools"> |
| 10 <xrefs> | 9 <xrefs> |
| 11 <xref type="bio.tools">trinity</xref> | 10 <xref type="bio.tools">trinity</xref> |
| 12 </xrefs> | 11 </xrefs> |
| 13 </xml> | 12 </xml> |
| 14 <token name="@WRAPPER_VERSION@">2.9.1</token> | 13 <token name="@TOOL_VERSION@">2.15.1</token> |
| 14 <token name="@VERSION_SUFFIX@">0</token> | |
| 15 | 15 |
| 16 <token name="@COMMAND_PAIRED_STRAND_JACCARD@"> | 16 <token name="@COMMAND_PAIRED_STRAND_JACCARD@"> |
| 17 #if $pool.inputs.strand.is_strand_specific: | 17 #if $pool.inputs.strand.is_strand_specific == 'true': |
| 18 --SS_lib_type $pool.inputs.strand.library_type | 18 --SS_lib_type $pool.inputs.strand.library_type |
| 19 #end if | 19 #end if |
| 20 | 20 |
| 21 $pool.inputs.jaccard_clip | 21 $pool.inputs.jaccard_clip |
| 22 </token> | 22 </token> |
| 23 | 23 |
| 24 <xml name="input_paired_strand_jaccard"> | 24 <xml name="input_paired_strand_jaccard"> |
| 25 <conditional name="strand"> | 25 <conditional name="strand"> |
| 26 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> | 26 <param name="is_strand_specific" type="select" label="Strand specific data"> |
| 27 <option value="false">No</option> | |
| 28 <option value="true">Yes</option> | |
| 29 </param> | |
| 27 <when value="false" /> | 30 <when value="false" /> |
| 28 <when value="true"> | 31 <when value="true"> |
| 29 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type"> | 32 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type"> |
| 30 <option value="FR">Forward-Reverse</option> | 33 <option value="FR">Forward-Reverse</option> |
| 31 <option value="RF">Reverse-Forward</option> | 34 <option value="RF">Reverse-Forward</option> |
| 33 </when> | 36 </when> |
| 34 </conditional> | 37 </conditional> |
| 35 <param argument="--jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="Set if you expect high gene density with UTR overlap"/> | 38 <param argument="--jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="Set if you expect high gene density with UTR overlap"/> |
| 36 </xml> | 39 </xml> |
| 37 | 40 |
| 41 <xml name="is_strand_specific_f_r"> | |
| 42 <conditional name="strand"> | |
| 43 <param name="is_strand_specific" type="select" label="Strand specific data"> | |
| 44 <option value="false">No</option> | |
| 45 <option value="true">Yes</option> | |
| 46 </param> | |
| 47 <when value="false"/> | |
| 48 <when value="true"> | |
| 49 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> | |
| 50 <option value="F">F</option> | |
| 51 <option value="R">R</option> | |
| 52 </param> | |
| 53 </when> | |
| 54 </conditional> | |
| 55 </xml> | |
| 56 | |
| 38 <xml name="citation"> | 57 <xml name="citation"> |
| 39 <citations> | 58 <citations> |
| 40 <citation type="doi">10.1038/nbt.1883</citation> | 59 <citation type="doi">10.1038/nbt.1883</citation> |
| 41 </citations> | 60 </citations> |
| 42 </xml> | 61 </xml> |