Mercurial > repos > yhoogstrate > featurecounts
changeset 8:1a288d568ac1 draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Thu, 19 Mar 2015 08:08:16 -0400 |
| parents | 2312bedfe2a3 |
| children | c74b27b17d73 |
| files | README.rst featurecounts.xml tool_dependencies.xml |
| diffstat | 3 files changed, 45 insertions(+), 26 deletions(-) [+] |
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--- a/README.rst Wed Nov 19 10:07:59 2014 -0500 +++ b/README.rst Thu Mar 19 08:08:16 2015 -0400 @@ -11,6 +11,7 @@ ----------- * Repository-Maintainer: Youri Hoogstrate +* Repository-Developers: Youri Hoogstrate, Marius van den Beek * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools @@ -51,3 +52,8 @@ You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>. + +Acknowledgements +---------------- + +I would like to thank Marius van den Beek for his contributions to this project. \ No newline at end of file
--- a/featurecounts.xml Wed Nov 19 10:07:59 2014 -0500 +++ b/featurecounts.xml Thu Mar 19 08:08:16 2015 -0400 @@ -1,22 +1,22 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="featurecounts" name="featureCounts" version="1.4.4.a"> +<tool id="featurecounts" name="featureCounts" version="1.4.6.p1"> <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> <requirements> - <requirement type="package" version="1.4.4">featurecounts</requirement> + <requirement type="package" version="1.4.6.p1">featurecounts</requirement> <requirement type="package" version="1.0.0">featurecounts2bed</requirement> </requirements> <version_command>featureCounts -v</version_command> <command> - <!-- + #* The following script is written in the "Cheetah" language: http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html - --> + *# - <!-- Check 01: do the alignments have a dbkey and is the option set to using it? --> + ## Check 01: do the alignments have a dbkey and is the option set to using it? #if $reference_gene_sets_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1 echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/gene_sets.loc' is configured properly!" >&2 #else - <!-- Check 02: are all alignments from the same type (bam || sam) --> + ## Check 02: are all alignments from the same type (bam || sam) #if len({ alignment.extension:True for alignment in $alignments }.keys()) != 1 echo "Either all files must be SAM or all files must be BAM, no mixture is allowed." >&2 #else @@ -29,12 +29,12 @@ #else if $reference_gene_sets_source.source_select == "history" "$reference_gene_sets_source.reference_gene_sets" #else - <!-- + #* This is a workaround to obtain the "genome.fa" file that corresponds to the dbkey of the alignments. Because this file is "calculated" during run-time, it can be used in a workflow. - --> + *# "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'gene_sets' ].get_fields() )[0][2] }" #end if @@ -64,15 +64,17 @@ 2>&1 + #set $columns = [str(i+7) for i, alignment in enumerate($alignments)] + #set $columns=",".join($columns) #if $format == "tabdel_default" or $format.value == "tabdel_default" ; cp $output tmp.txt ; egrep -v "^#" tmp.txt > tmp2.txt - ; cut -f 1,7 tmp2.txt > tmp_left.txt + ; cut -f 1,$columns tmp2.txt > tmp_left.txt ; cut -f 6 tmp2.txt > tmp_right.txt ; paste tmp_left.txt tmp_right.txt > $output #elif $format == "tabdel_short" or $format.value == "tabdel_short" ; cp $output tmp.txt - ; egrep -v "^#" tmp.txt | cut -f 1,7 > $output + ; egrep -v "^#" tmp.txt | cut -f 1,$columns > $output #end if ## For every alignment, replace its filename for: "hid: sample name" @@ -191,9 +193,13 @@ <outputs> <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> - <data format="text" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" /> + <data format="tabular" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" /> </outputs> - + + <tests> + <test> + </test> + </tests> <help> featureCounts ############# @@ -222,17 +228,6 @@ 2. Make sure that your gene_sets.loc is configured properly as data table. This is generally done by copying the right information into: tool_data_table_conf.xml. More info at: https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables -References ----------- - -**featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.** - -*Liao Y1, Smyth GK, Shi W.* - Bioinformatics. 2014 Apr 1;30(7):923-30. - -- http://www.ncbi.nlm.nih.gov/pubmed/24227677 -- http://dx.doi.org/10.1093/bioinformatics/btt656 - - License ------- @@ -257,5 +252,23 @@ http://toolshed.g2.bx.psu.edu/ http://testtoolshed.g2.bx.psu.edu/ + +References +---------- +**featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.** + +*Liao Y1, Smyth GK, Shi W.* - Bioinformatics. 2014 Apr 1;30(7):923-30. + +- http://www.ncbi.nlm.nih.gov/pubmed/24227677 +- http://dx.doi.org/10.1093/bioinformatics/btt656 + + +Acknowledgements +---------------- + +I would like to thank Marius van den Beek for his contributions to this project. </help> +<citations> + <citation type="doi">10.1093/bioinformatics/btt656</citation> +</citations> </tool>
--- a/tool_dependencies.xml Wed Nov 19 10:07:59 2014 -0500 +++ b/tool_dependencies.xml Thu Mar 19 08:08:16 2015 -0400 @@ -1,11 +1,11 @@ <?xml version="1.0"?> <tool_dependency> - <package name="featurecounts" version="1.4.4"> + <package name="featurecounts" version="1.4.6.p1"> <install version="1.0"> <actions> - <action type="shell_command">wget http://sourceforge.net/projects/subread/files/subread-1.4.4/subread-1.4.4-source.tar.gz && tar -zxvf subread-1.4.4-source.tar.gz && cd subread-1.4.4-source/src/ && make -f Makefile.Linux && cd ../../</action> + <action type="shell_command">wget http://garr.dl.sourceforge.net/project/subread/subread-1.4.6-p1/subread-1.4.6-p1-source.tar.gz && tar -zxvf subread-1.4.6-p1-source.tar.gz && cd subread-1.4.6-p1-source/src/ && make -f Makefile.Linux && cd ../../</action> <action type="move_file"> - <source>../subread-1.4.4-source/bin/featureCounts</source> + <source>../subread-1.4.6-p1-source/bin/featureCounts</source> <destination>$INSTALL_DIR/bin/</destination> </action> <action type="set_environment">