Mercurial > repos > padge > trimal
comparison trimal.xml @ 2:0d53577b962f draft
"planemo upload for repository https://github.com/inab/trimal commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
| author | padge |
|---|---|
| date | Mon, 11 Apr 2022 13:07:11 +0000 |
| parents | b15a3147e604 |
| children | 4769baf47b8d |
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| 1:98944ec4bfc7 | 2:0d53577b962f |
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| 13 #end if | 13 #end if |
| 14 ; | 14 ; |
| 15 | 15 |
| 16 ]]></command> | 16 ]]></command> |
| 17 <inputs> | 17 <inputs> |
| 18 <param name="input1" type="data" format="fasta,clustal,pir,phylip,nexus" multiple="false" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" optional="false" /> | 18 <param name="input1" type="data" format="fasta,clustal,pir,phylip,nexus,mega" multiple="false" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" optional="false" /> |
| 19 <conditional name="trimming_mode"> | 19 <conditional name="trimming_mode"> |
| 20 <param name="mode_selector" type="select" label="Select trimming mode from the list"> | 20 <param name="mode_selector" type="select" label="Select trimming mode from the list"> |
| 21 <option value="-nogaps">nogaps. Remove all positions with gaps in the alignment.</option> | 21 <option value="-nogaps">nogaps. Remove all positions with gaps in the alignment.</option> |
| 22 <option value="-noallgaps">noallgaps. Remove columns composed only by gaps.</option> | 22 <option value="-noallgaps">noallgaps. Remove columns composed only by gaps.</option> |
| 23 <option value="-gappyout">gappyout. Only uses information based on gaps' distribution. (see User Guide)</option> | 23 <option value="-gappyout">gappyout. Only uses information based on gaps' distribution. (see User Guide)</option> |
| 46 <option value="-phylip3.2">PHYLIP3.2 format</option> | 46 <option value="-phylip3.2">PHYLIP3.2 format</option> |
| 47 <option value="-phylip3.2_m10">PHYLIP3.2 format. Sequences name length up to 10 characters.</option> | 47 <option value="-phylip3.2_m10">PHYLIP3.2 format. Sequences name length up to 10 characters.</option> |
| 48 </param> | 48 </param> |
| 49 </inputs> | 49 </inputs> |
| 50 <outputs> | 50 <outputs> |
| 51 <data name="trimmed_output" format="fasta" label="Trimmed alignment."/> | 51 <data name="trimmed_output" format="fasta" label="Trimmed alignment."> |
| 52 <change_format> | |
| 53 <when input="out_format_selector" value="-fasta" format="fasta" /> | |
| 54 <when input="out_format_selector" value="-fasta_m10" format="fasta" /> | |
| 55 <when input="out_format_selector" value="-phylip" format="phylip" /> | |
| 56 <when input="out_format_selector" value="-phylip_m10" format="phylip" /> | |
| 57 <when input="out_format_selector" value="-phylip_paml" format="phylip" /> | |
| 58 <when input="out_format_selector" value="-phylip_paml_m10" format="phylip" /> | |
| 59 <when input="out_format_selector" value="-phylip3.2" format="phylip" /> | |
| 60 <when input="out_format_selector" value="-phylip3.2_m10" format="phylip" /> | |
| 61 <when input="out_format_selector" value="-clustal" format="clustal" /> | |
| 62 <when input="out_format_selector" value="-mega" format="mega" /> | |
| 63 <when input="out_format_selector" value="-nbrf" format="pir" /> | |
| 64 <when input="out_format_selector" value="-nexus" format="nexus" /> | |
| 65 </change_format> | |
| 66 </data> | |
| 52 <data name="html_summary" format="html" label="trimal html summary."/> | 67 <data name="html_summary" format="html" label="trimal html summary."/> |
| 53 </outputs> | 68 </outputs> |
| 54 <tests> | 69 <tests> |
| 55 <test> | 70 <test> |
| 56 <param name="input1" value="example.009.AA.fasta"/> | 71 <param name="input1" value="example.009.AA.fasta"/> |