diff gtf2featureAnnotation.xml @ 7:14b3f2a4523b draft default tip

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"

--- a/gtf2featureAnnotation.xml	Wed Mar 04 06:44:32 2020 -0500
+++ b/gtf2featureAnnotation.xml	Mon Jul 19 08:00:24 2021 +0000
@@ -1,13 +1,11 @@
-<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy6" profile="18.01">
+<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.52.0+galaxy0" profile="18.01">
     <description>extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer</description>
     <requirements>
-      <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement>
-      <requirement type="package" version="2.50.2">bioconductor-biostrings</requirement>
-      <requirement type="package" version="1.6.4">r-optparse</requirement>
+      <requirement type="package" version="1.0.1">atlas-gene-annotation-manipulation</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
        ln -s '$gtf_input' input.gtf;
-       $__tool_directory__/gtf2featureAnnotation.R --gtf-file input.gtf
+       gtf2featureAnnotation.R --gtf-file input.gtf
 #if $noheader
 --no-header
 #end if
@@ -17,8 +15,17 @@
 #if $mito.mark_mito
 --mito --mito-chr "${mito.mito_chr}" --mito-biotypes "${mito.mito_biotypes}"
 #end if
+#if $cdnas.parse_cdnas
+--parse-cdnas "${cdnas.fasta_input}" --parse-cdna-field "${cdnas.cdnas_field}" 
 #if $cdnas.filter_cdnas
---filter-cdnas "${cdnas.fasta_input}" --filter-cdnas-field "${cdnas.cdnas_field}" --filter-cdnas-output "${fasta_output}"
+--filter-cdnas-output "${fasta_output}"
+#end if
+#if $cdnas.parse_cdna_names
+--parse-cdna-names
+#end if
+#if $fill_empty
+--fill-empty "${fill_empty}"
+#end if
 #end if
 --feature-type "${feature_type}" --first-field "${first_field}" --output-file annotation.txt --fields "${fields}"
 	    ]]></command>
@@ -30,6 +37,7 @@
         <param name="noheader" type="boolean" checked="false" label="Suppress header line in output?"/>
         <param name="fields" type="text" optional='true' value="" label="Comma-separated list of field names to extract from the GTF (default: use all fields)"/>
         <param name="version_transcripts" type="boolean" checked="false" label="Append version to transcript identifiers?" help="For transcript feature type only: where the GTF contains transcript versions, should these be appended to transcript identifiers? Useful when generating transcript/gene mappings for use with transcriptomes"/>
+        <param name="fill_empty" type="text" optional='true' value="" label="Column to be used to fill empty values in other fields" help="Only when output fields are defined, useful when you need to guarantee a value, for example a gene ID for a transcript/gene mapping."/>
         <conditional name="mito">
           <param name="mark_mito" type="boolean" checked="true" label="Flag mitochondrial features?"/>
           <when value="true">
@@ -39,10 +47,12 @@
           <when value="false" />
         </conditional>
         <conditional name="cdnas">
-          <param name="filter_cdnas" type="boolean" checked="false" label="Filter a FASTA-format cDNA file to match annotations?" help="For some applications, e.g. transcriptome mappers, its useful to match a cDNAs file to an annotation list (e.g. transcript-to-gene mapping)"/>
+          <param name="parse_cdnas" type="boolean" checked="false" label="Provide a cDNA file for extracting annotations and/ or possible filtering?" help="For some applications, e.g. transcriptome mappers, its useful to match a cDNAs file to an annotation list (e.g. transcript-to-gene mapping)"/>
           <when value="true">
             <param name="fasta_input" type="data" format="fasta,fasta.gz" label="FASTA-format cDNA/ transcript file" />
-            <param name="cdnas_field" type="text" optional='true' value="transcript_id" label="Annotation field to match with sequences."/>
+            <param name="cdnas_field" type="text" optional='true' value="transcript_id" label="Annotation field in GTF to match with sequences."/>
+            <param name="parse_cdna_names" type="boolean" checked="false" label="Parse the FASTA headers for annotation info?" help="e.g. to find gene IDs for transcripts not present in the GTF. May only work for Ensembl GTFs."/>
+            <param name="filter_cdnas" type="boolean" checked="false" label="Filter the cDNA file to match the annotations?" />
           </when>
           <when value="false" />
         </conditional>
@@ -67,9 +77,9 @@
 
 **What it does**
 
-Given an Ensembl GTF file, it will extract all information on chromosomes, coordinates, and attributes provided at the specified feature level. Mitochondrial features can also be flagged.
+Given an Ensembl GTF file, it will extract all information on chromosomes, coordinates, and attributes provided at the specified feature level. Mitochondrial features can also be flagged. See https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation.
 
-You can also supply a fasta-format file of sequences, which will be filtered by identifier to match annotation. This can be useful for tools such as Alevin which need a transcript-to-gene mapping and a transcriptome file without any missing entries (with respect to annotation).
+You can also supply a fasta-format file of sequences, which can be filtered by identifier to match annotation and/or used a source of information for transcripts un-annotated in the GTF. This can be useful for tools such as Alevin which need a transcript-to-gene mapping and a transcriptome file without any missing entries (with respect to annotation).
 
 
 **Inputs**
@@ -92,5 +102,6 @@
 journal = {GitHub repository},
 url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary},
   }</citation>
+  <citation type="doi">10.1101/2020.04.08.032698</citation>
 </citations>
 </tool>