| Previous changeset 2:a80f96e55958 (2016-10-31) Next changeset 4:d417fb66494e (2017-01-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f |
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modified:
featurecounts.xml |
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added:
tool-data/gene_sets.loc.sample tool_data_table_conf.xml.sample |
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| diff -r a80f96e55958 -r dae123c03a74 featurecounts.xml --- a/featurecounts.xml Mon Oct 31 07:26:54 2016 -0400 +++ b/featurecounts.xml Thu Nov 10 03:05:17 2016 -0500 |
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| b'@@ -8,7 +8,12 @@\n <command><![CDATA[\n ## Check whether all alignments are from the same type (bam || sam)\n featureCounts\n- -a "$reference_gene_sets"\n+ #if $gtf_source.ref_source=="history":\n+ -a "$gtf_source.reference_gene_sets"\n+ #else:\n+ -a "$gtf_source.reference_gene_sets_builtin.fields.path"\n+ #end if\n+\n -o "output"\n -T \\${GALAXY_SLOTS:-2}\n \n@@ -25,7 +30,7 @@\n \n -Q $extended_parameters.mapping_quality\n $extended_parameters.largest_overlap\n- --minOverlap $extended_parameters.min_overlap\n+ --minOverlap $extended_parameters.min_overlap\n $extended_parameters.read_reduction\n $extended_parameters.primary\n $extended_parameters.ignore_dup\n@@ -87,11 +92,27 @@\n label="Alignment file"\n help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format" />\n \n- <param name="reference_gene_sets"\n- format="gff,gtf,gff3"\n- type="data"\n- label="Gene annotation file"\n- help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment" />\n+ <conditional name="gtf_source">\n+ <param name="ref_source" type="select" label="Gene annotation file">\n+ <option value="cached">locally cached</option>\n+ <option value="history">in your history</option>\n+ </param>\n+ <when value="cached">\n+ <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator">\n+ <options from_data_table="gene_sets">\n+ <filter type="sort_by" column="1" />\n+ <validator type="no_options" message="No annotations are available." />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="reference_gene_sets"\n+ format="gff,gtf,gff3"\n+ type="data"\n+ label="Gene annotation file"\n+ help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment" />\n+ </when>\n+ </conditional>\n \n <param name="format"\n type="select"\n@@ -208,7 +229,7 @@\n falsevalue=""\n argument="-O"\n label="Allow read to contribute to multiple features"\n- help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta- feature (or matched feature if -f is specified)" />\n+ help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta-feature (or matched feature if -f is specified)" />\n \n <param name="strand_specificity"\n type="select"\n@@ -281,7 +302,7 @@\n type="select"\n label="Reduce read to single position"\n argument="--read2pos"\n- help="The read is reduced to its 5\' most base or 3\'most base. Read summarization is then performed based on thesingle base which the read is reduced to.">\n+ help="The read is reduced to its 5\' most base or 3\'most base. Read summarization is then performed based on the single base the the read is reduced to.">\n <option value="" selected="tru'..b' that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read." />\n \n <param name="count_split_alignments_only"\n type="boolean"\n truevalue=" --countSplitAlignmentsOnly"\n falsevalue=""\n argument="--countSplitAlignmentsOnly"\n- label="Ignore reads marked as duplicate"\n- help="If specified, only split alignments (CIGARstrings containing letter `N\') will be counted. All the otheralignments will be ignored. An example of split alignments isthe exon-spanning reads in RNA-seq data." />\n+ label="Ignore unspliced alignments"\n+ help="If specified, only split alignments (CIGAR strings containing the letter `N\') will be counted. All the other alignments will be ignored. An example of split alignments are exon-spanning reads in RNA-seq data." />\n </section>\n </inputs>\n <outputs>\n@@ -364,6 +385,7 @@\n <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />\n <param name="format" value="tabdel_short" />\n <param name="include_feature_length_file" value="true"/>\n+ <param name="ref_source" value="history" />\n <output name="output" file="output_1_short.tab"/>\n <output name="output_summary" file="output_1_summary.tab"/>\n </test>\n@@ -372,6 +394,7 @@\n <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />\n <param name="format" value="tabdel_medium" />\n <param name="include_feature_length_file" value="true"/>\n+ <param name="ref_source" value="history" />\n <output name="output" file="output_1_medium.tab"/>\n <output name="output_summary" file="output_1_summary.tab"/>\n </test>\n@@ -380,6 +403,7 @@\n <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />\n <param name="format" value="tabdel_full" />\n <param name="include_feature_length_file" value="true"/>\n+ <param name="ref_source" value="history" />\n <output name="output" file="output_1_full.tab"/>\n <output name="output_summary" file="output_1_summary.tab"/>\n <output name="output_feature_lengths" file="output_feature_lengths.tab"/>\n@@ -390,6 +414,7 @@\n <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />\n <param name="format" value="tabdel_short" />\n <param name="include_feature_length_file" value="true"/>\n+ <param name="ref_source" value="history" />\n <output name="output" file="output_2_short.tab"/>\n <output name="output_summary" file="output_2_summary.tab"/>\n </test>\n@@ -398,6 +423,7 @@\n <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />\n <param name="format" value="tabdel_medium" />\n <param name="include_feature_length_file" value="true"/>\n+ <param name="ref_source" value="history" />\n <output name="output" file="output_2_medium.tab"/>\n <output name="output_summary" file="output_2_summary.tab"/>\n </test>\n@@ -406,6 +432,7 @@\n <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />\n <param name="format" value="tabdel_full" />\n <param name="include_feature_length_file" value="true"/>\n+ <param name="ref_source" value="history" />\n <output name="output" file="output_2_full.tab"/>\n <output name="output_summary" file="output_2_summary.tab"/>\n <output name="output_feature_lengths" file="output_feature_lengths.tab"/>\n' |
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| diff -r a80f96e55958 -r dae123c03a74 tool-data/gene_sets.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gene_sets.loc.sample Thu Nov 10 03:05:17 2016 -0500 |
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| @@ -0,0 +1,14 @@ +# This is a sample file distributed with featureCounts that enables it and other# tools to use gene/exon annotations in the GFF/GTF format. +# +# The gene_sets.loc file syntax is: +#<unique_build_id> <dbkey> <display_name> <path> +# +# Please ensure that the above fields are tab separated. +# +# In case you have TWO or MORE providers PER dbkey, the one mentioned +# first in the file, should have the "default" priority. +# +#Example: +# +#Homo_sapiens.GRCh37.74 hg19 GRCh37 (hg19) annotation from Ensembl, release 74 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf +#Homo_sapiens.NCBI36.54 hg18 hg18 annotation from Ensembl, release 54 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf |
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| diff -r a80f96e55958 -r dae123c03a74 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Nov 10 03:05:17 2016 -0500 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Location of all GFF/GTF files --> + <table name="gene_sets" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/gene_sets.loc" /> + </table> +</tables> |