Mercurial > repos > iuc > tracy_assemble
comparison macros.xml @ 0:99d31ec6629b draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
| author | iuc |
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| date | Tue, 12 Oct 2021 14:20:41 +0000 |
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| -1:000000000000 | 0:99d31ec6629b |
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| 1 <macros> | |
| 2 <token name="@TOOL_VERSION@">0.6.1</token> | |
| 3 <xml name="requirements"> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="@TOOL_VERSION@">tracy</requirement> | |
| 6 <yield/> | |
| 7 </requirements> | |
| 8 </xml> | |
| 9 <xml name="citations"> | |
| 10 <citations> | |
| 11 <citation type="doi">10.1186/s12864-020-6635-8</citation> | |
| 12 <yield /> | |
| 13 </citations> | |
| 14 </xml> | |
| 15 <xml name="version_command"> | |
| 16 <version_command>tracy --version</version_command> | |
| 17 </xml> | |
| 18 <xml name="common_options"> | |
| 19 <param argument="--pratio" type="float" value="0.33" label="Peak ratio to call base" /> | |
| 20 <param argument="--maxindel" type="integer" value="1000" label="Maximum indel size in Sanger trace" min="1" /> | |
| 21 <param argument="--linelimit" type="integer" value="60" label="Alignment line length" min="1" /> | |
| 22 </xml> | |
| 23 <xml name="kmer_options"> | |
| 24 <section name="kmer" title="Kmer options"> | |
| 25 <param argument="--kmer" type="integer" value="15" label="Kmer size to anchor trace" min="1" /> | |
| 26 <param argument="--support" type="integer" value="3" label="Minimum kmer support" min="1" /> | |
| 27 </section> | |
| 28 </xml> | |
| 29 <xml name="trim_options"> | |
| 30 <section name="trim" title="Trimming options"> | |
| 31 <param argument="--trim" type="integer" value="0" label="Trimming stringency (0: use trimLeft and trimRight)" /> | |
| 32 <param argument="--trimLeft" type="integer" value="50" label="Trim size left" min="0" /> | |
| 33 <param argument="--trimRight" type="integer" value="50" label="Trim size right" min="0" /> | |
| 34 </section> | |
| 35 </xml> | |
| 36 <xml name="alignment_options"> | |
| 37 <section name="alignment" title="Alignment options"> | |
| 38 <param argument="--gapopen" type="integer" value="-10" max="0" label="Gap open penalty" /> | |
| 39 <param argument="--gapext" type="integer" value="-4" max="0" label="Gap extension penalty" /> | |
| 40 <param argument="--match" type="integer" value="3" min="0" label="Match score" /> | |
| 41 <param argument="--mismatch" type="integer" value="-5" max="0" label="Mismatch penalty" /> | |
| 42 </section> | |
| 43 </xml> | |
| 44 <token name="@pratio@"><![CDATA[ | |
| 45 The *pratio* parameter is a floating point value expressing the minimum proportion of the maximum trace value that will still be | |
| 46 called as a base. For example, if the maximum value found in the trace file is 10, and pratio is 0.3, a peak needs to be | |
| 47 higher than 3 to be called as a base. | |
| 48 ]]></token> | |
| 49 <token name="@trim_options@"><![CDATA[ | |
| 50 Prior to alignment the trace file is trimmed. Either a fixed number of bases can be trimmed from the left or right sides of | |
| 51 the trace, or trimming points (on the left or right or the trace) can be automatically found using an algorithm that works | |
| 52 outwards from the best 10% of the trace and uses a sliding window (of size 10 bases) to find the point where the trace | |
| 53 quality falls below a computed threshold. This automated trimming algorithm can be tuned using a *trimming stringency* (higher | |
| 54 values mean stricter trimming). | |
| 55 ]]></token> | |
| 56 <token name="@alignment@"><![CDATA[ | |
| 57 The dynamic programming step of the alignment uses the `Gotoh's algorithm <http://rna.informatik.uni-freiburg.de/Teaching/index.jsp?toolName=Gotoh>`_ | |
| 58 which can be tuned using scores for nucleotide matches, mismatches, gap opening and gap extension. | |
| 59 ]]></token> | |
| 60 <xml name="optional_outputs"> | |
| 61 <param name="optional_outputs" type="select" multiple="true" label="Optional outputs"> | |
| 62 <option value="json">JSON</option> | |
| 63 <option value="tabular">tabular statistics report</option> | |
| 64 </param> | |
| 65 </xml> | |
| 66 <xml name="json_output" token_toolname=""> | |
| 67 <data name="out_json" format="json" from_work_dir="out.json" label="tracy @TOOLNAME@ JSON on ${on_string}"> | |
| 68 <filter>optional_outputs and 'json' in optional_outputs</filter> | |
| 69 </data> | |
| 70 </xml> | |
| 71 <xml name="tabular_output" token_toolname=""> | |
| 72 <data name="out_stats" format="tabular" from_work_dir="out.abif" label="tracy @TOOLNAME@ stats on ${on_string}"> | |
| 73 <actions> | |
| 74 <action name="column_names" type="metadata" default="pos,peakA,peakC,peakG,peakT,basenum,primary,secondary,consensus,qual,trim" /> | |
| 75 </actions> | |
| 76 <filter>optional_outputs and 'tabular' in optional_outputs</filter> | |
| 77 </data> | |
| 78 </xml> | |
| 79 </macros> |