Mercurial > repos > earlhaminst > gstf_preparation

comparison gstf_preparation.xml @ 8:92f3966d5bc3 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 88ba62ae8c3d9587a0015c72209242ad0c1df0c2
author earlhaminst
date Wed, 16 May 2018 20:03:57 -0400
parents 9ef7661e8e9c
children e8e75a79de59
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7:9ef7661e8e9c 8:92f3966d5bc3
35 <param name="genome" type="text" label="Genome name" help="Genome name without whitespaces or special characters"> 35 <param name="genome" type="text" label="Genome name" help="Genome name without whitespaces or special characters">
36 <validator type="empty_field" /> 36 <validator type="empty_field" />
37 </param> 37 </param>
38 </repeat> 38 </repeat>
39 <param name="json" type="data" format="json" multiple="true" optional="true" label="Gene features in JSON format generated by 'Get features by Ensembl ID' tool" /> 39 <param name="json" type="data" format="json" multiple="true" optional="true" label="Gene features in JSON format generated by 'Get features by Ensembl ID' tool" />
40 <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding FASTA datasets" help="Each FASTA header line should start with a transcript id" /> 40 <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding CDS datasets in FASTA format" help="Each FASTA header line should start with a transcript id" />
41 <param name="longestCDS" type="boolean" checked="false" label="Keep only the longest CDS per gene" /> 41 <param name="longestCDS" type="boolean" checked="false" label="Keep only the longest CDS per gene" />
42 <param name="headers" type="boolean" checked="true" label="Change the header line of the FASTA sequences to the &gt;TranscriptId_species format" help="As required by TreeBest, part of the GeneSeqToFamily workflow" /> 42 <param name="headers" type="boolean" checked="true" label="Change the header line of the FASTA sequences to the &gt;TranscriptId_species format" help="As required by TreeBest, part of the GeneSeqToFamily workflow" />
43 <param name="regions" type="text" optional="true" label="Comma-separated list of region IDs (e.g. chromosomes or scaffolds) for which FASTA sequences should be filtered" help="Region IDs are in the `seqid` column for GFF3 and in the `seq_region_name` field in JSON. This is typically used to filter chromosomes with a non-standard genetic code, like mitochondria, to be analysed separately" /> 43 <param name="regions" type="text" optional="true" label="Comma-separated list of region IDs (e.g. chromosomes or scaffolds) for which FASTA sequences should be filtered" help="Region IDs are in the `seqid` column for GFF3 and in the `seq_region_name` field in JSON. This is typically used to filter chromosomes with a non-standard genetic code, like mitochondria, to be analysed separately" />
44 </inputs> 44 </inputs>
45 45
109 <![CDATA[ 109 <![CDATA[
110 **What it does** 110 **What it does**
111 111
112 This tool converts a set of GFF3 and/or JSON gene feature information datasets into SQLite format. 112 This tool converts a set of GFF3 and/or JSON gene feature information datasets into SQLite format.
113 113
114 It also filters a CDS FASTA dataset to keep only the transcripts present in the gene feature information. Optionally it can also keep only the longest CDS per gene and/or change the header line of the FASTA sequences to the >TranscriptId_species format (as required by TreeBest, part of the GeneSeqToFamily workflow). 114 It also filters the CDS FASTA datasets to:
115
116 - remove coding sequences whose length is not a multiple of 3
117 - keep only the transcripts present in the gene feature information.
118
119 Optionally it can also keep only the longest CDS per gene and/or change the header line of the FASTA sequences to the >TranscriptId_species format (as required by TreeBest, part of the GeneSeqToFamily workflow).
115 120
116 Example GFF3 file:: 121 Example GFF3 file::
117 122
118 scaffold_0 MYZPE13164_Clone_G006_v1.0 gene 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030;biotype=protein_coding 123 scaffold_0 MYZPE13164_Clone_G006_v1.0 gene 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030;biotype=protein_coding
119 scaffold_0 MYZPE13164_Clone_G006_v1.0 mRNA 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1;Parent=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030.1;biotype=protein_coding;_AED=0.31 124 scaffold_0 MYZPE13164_Clone_G006_v1.0 mRNA 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1;Parent=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030.1;biotype=protein_coding;_AED=0.31