Mercurial > repos > iuc > fastp
comparison macros.xml @ 11:d5ae828d1c3c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f
| author | iuc |
|---|---|
| date | Tue, 13 Aug 2024 12:18:28 +0000 |
| parents | 75d9fef449c7 |
| children | 6292d4ff1ddd |
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| 10:75d9fef449c7 | 11:d5ae828d1c3c |
|---|---|
| 1 <macros> | 1 <macros> |
| 2 <token name="@WRAPPER_VERSION@">0.23.2</token> | 2 <token name="@TOOL_VERSION@">0.23.4</token> |
| 3 | 3 <xml name="biotools"> |
| 4 <xrefs> | |
| 5 <xref type="bio.tools"> | |
| 6 fastp | |
| 7 </xref> | |
| 8 </xrefs> | |
| 9 </xml> | |
| 4 <xml name="adapter_trimming_options"> | 10 <xml name="adapter_trimming_options"> |
| 5 <section name="adapter_trimming_options" title="Adapter Trimming Options" expanded="False"> | 11 <section name="adapter_trimming_options" title="Adapter Trimming Options" expanded="False"> |
| 6 <param name="disable_adapter_trimming" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Disable adapter trimming" help="Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled."/> | 12 <param name="disable_adapter_trimming" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Disable adapter trimming" help="Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled."/> |
| 7 <expand macro="adapter_sequence" read_number="1" /> | 13 <expand macro="adapter_sequence" read_number="1" /> |
| 8 <yield /> | 14 <yield /> |
| 9 </section> | |
| 10 <section name="global_trimming_options" title="Global Trimming Options" expanded="False"> | |
| 11 <param name="trim_front1" argument="-f" type="integer" optional="true" label="Trim front for input 1" help="Trimming how many bases in front for read1, default is 0."/> | |
| 12 <param name="trim_tail1" argument="-t" type="integer" optional="true" label="Trim tail for input 1" help="Trimming how many bases in tail for read1, default is 0."/> | |
| 13 </section> | 15 </section> |
| 14 </xml> | 16 </xml> |
| 15 | 17 |
| 16 <xml name="global_trimming_options"> | 18 <xml name="global_trimming_options"> |
| 17 <section name="global_trimming_options" title="Global trimming options" expanded="False"> | 19 <section name="global_trimming_options" title="Global trimming options" expanded="False"> |
| 27 <param name="trim_tail2" argument="-T" type="integer" optional="true" label="Trim tail for input 2" help="Trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings."/> | 29 <param name="trim_tail2" argument="-T" type="integer" optional="true" label="Trim tail for input 2" help="Trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings."/> |
| 28 </expand> | 30 </expand> |
| 29 </xml> | 31 </xml> |
| 30 | 32 |
| 31 <xml name="adapter_sequence" token_read_number="1"> | 33 <xml name="adapter_sequence" token_read_number="1"> |
| 32 <param name="adapter_sequence@READ_NUMBER@" argument="--adapter_sequence@READ_NUMBER@" type="text" optional="true" label="Adapter sequence for input @READ_NUMBER@" help="The adapter for read@READ_NUMBER@. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped."> | 34 <param argument="--adapter_sequence@READ_NUMBER@" type="text" optional="true" label="Adapter sequence for input @READ_NUMBER@" help="The adapter for read@READ_NUMBER@. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped."> |
| 33 <sanitizer> | 35 <sanitizer> |
| 34 <valid> | 36 <valid> |
| 35 <add value="A"/> | 37 <add value="A"/> |
| 36 <add value="T"/> | 38 <add value="T"/> |
| 37 <add value="C"/> | 39 <add value="C"/> |
| 39 </valid> | 41 </valid> |
| 40 </sanitizer> | 42 </sanitizer> |
| 41 </param> | 43 </param> |
| 42 </xml> | 44 </xml> |
| 43 | 45 |
| 46 <xml name="detect_adapter_for_pe"> | |
| 47 <param argument="--detect_adapter_for_pe" type="boolean" truevalue="--detect_adapter_for_pe" falsevalue="" checked="false" label="Adapter sequence auto-detection for paired-end" /> | |
| 48 </xml> | |
| 49 | |
| 44 <xml name="in" token_read_number="1" token_argument="-i"> | 50 <xml name="in" token_read_number="1" token_argument="-i"> |
| 45 <param name="in@READ_NUMBER@" argument="@ARGUMENT@" type="data" format="fastq,fastq.gz" label="Input @READ_NUMBER@" help="Input FASTQ file #@READ_NUMBER@"/> | 51 <param name="in@READ_NUMBER@" argument="@ARGUMENT@" type="data" format="fastq,fastq.gz" label="Input @READ_NUMBER@" help="Input FASTQ file #@READ_NUMBER@"/> |
| 46 </xml> | 52 </xml> |
| 47 | 53 |
| 48 <xml name="poly_g_min_len"> | 54 <xml name="poly_g_min_len"> |
| 49 <param name="poly_g_min_len" argument="--poly_g_min_len" type="integer" optional="true" label="PolyG minimum length" | 55 <param argument="--poly_g_min_len" type="integer" optional="true" label="PolyG minimum length" |
| 50 help="The minimum length to detect polyG in the read tail. 10 by default."/> | 56 help="The minimum length to detect polyG in the read tail. 10 by default."/> |
| 51 </xml> | 57 </xml> |
| 52 </macros> | 58 </macros> |