Mercurial > repos > artbio > mircounts
changeset 4:da1aa7de2b19 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
| author | artbio |
|---|---|
| date | Mon, 04 Sep 2017 17:55:01 -0400 |
| parents | 6b8adacd4750 |
| children | 9ea96a02c416 |
| files | mircounts.py mircounts.xml test-data/mirs_clipped_count.tab test-data/mirs_unclipped_count.tab test-data/pre_mirs_clipped_count.tab test-data/pre_mirs_unclipped_count.tab |
| diffstat | 6 files changed, 53 insertions(+), 9 deletions(-) [+] |
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--- a/mircounts.py Wed Jul 26 19:15:08 2017 -0400 +++ b/mircounts.py Mon Sep 04 17:55:01 2017 -0400 @@ -104,7 +104,6 @@ writes a count table """ F = open(outfile, 'w') - F.write('Gene\tCounts\n') for gene in sorted(countdict): F.write('%s\t%s\n' % (gene, str(countdict[gene]))) F.close()
--- a/mircounts.xml Wed Jul 26 19:15:08 2017 -0400 +++ b/mircounts.xml Mon Sep 04 17:55:01 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="mircounts" name="miRcounts" version="0.9.3"> +<tool id="mircounts" name="miRcounts" version="0.9.4"> <description> Counts miRNA alignments from small RNA sequence data</description> <requirements> <requirement type="package" version="1.18">gnu-wget</requirement> @@ -9,7 +9,6 @@ <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - ## To be refactored with guidelines in https://github.com/ARTbio/tools-artbio/issues/140 wget ftp://mirbase.org/pub/mirbase/CURRENT/genomes/${genomeKey}.gff3 && ## download gff3 specified by the variable genomeKey python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript". wget ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.gz && @@ -75,6 +74,48 @@ <column name="value" index="0"/> </options> </param> + <!-- work on proper selection of the url (that varies between gff, gff2 and gff3) + <param name="mirbase_version" type="select" label="Choose miRbase version"> + <option selected="true" value="CURRENT">Current</option> + <option value="1.0">1.0</option> + <option value="1.1">1.1</option> + <option value="1.2">1.2</option> + <option value="1.3">1.3</option> + <option value="1.4">1.4</option> + <option value="1.5">1.5</option> + <option value="2.0">2.0</option> + <option value="2.1">2.0</option> + <option value="2.2">2.2</option> + <option value="3.0">3.0</option> + <option value="3.1">3.1</option> + <option value="4.0">4.0</option> + <option value="5.0">5.0</option> + <option value="5.1">5.1</option> + <option value="6.0">6.0</option> + <option value="7.0">7.0</option> + <option value="7.1">7.1</option> + <option value="8.0">8.0</option> + <option value="8.1">8.1</option> + <option value="8.2">8.2</option> + <option value="9.0">9.0</option> + <option value="9.1">9.1</option> + <option value="9.2">9.2</option> + <option value="10.0">10.0</option> + <option value="10.1">10.1</option> + <option value="11.0">11.0</option> + <option value="12.0">12.0</option> + <option value="13.0">13.0</option> + <option value="14">14</option> + <option value="15">15</option> + <option value="16">16</option> + <option value="17">17</option> + <option value="18">18</option> + <option value="19">19</option> + <option value="20">20</option> + <option value="21">21</option> + </options> + </param> + --> <param help="command [ bowtie -v 0,1,2,3 -M 1 --best --strata --norc ] will be used. Specify a value for -v (number of mismatches allowed)" label="Number of mismatches allowed" name="v" type="select"> <option value="0">0</option> <option selected="true" value="1">1</option> @@ -99,8 +140,16 @@ <outputs> <data format="bam" label="BAM alignment" name="output" /> <data format="gff3" label="GFF3 generated by miRCounts" name="gff3"/> - <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file" /> - <data format="tabular" label="Mir Counts" name="mir_count_file" /> + <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file"> + <actions> + <action name="column_names" type="metadata" default="Gene,Counts" /> + </actions> + </data> + <data format="tabular" label="Mir Counts" name="mir_count_file"> + <actions> + <action name="column_names" type="metadata" default="Gene,Counts" /> + </actions> + </data> <data format="tabular" label="Coverage Table" name="coverage_dataframe"> <filter>plotting['plottingOption'] == "yes"</filter> </data>
--- a/test-data/mirs_clipped_count.tab Wed Jul 26 19:15:08 2017 -0400 +++ b/test-data/mirs_clipped_count.tab Mon Sep 04 17:55:01 2017 -0400 @@ -1,4 +1,3 @@ -Gene Counts dme-bantam-3p 8 dme-bantam-5p 0 dme-let-7-3p 0
--- a/test-data/mirs_unclipped_count.tab Wed Jul 26 19:15:08 2017 -0400 +++ b/test-data/mirs_unclipped_count.tab Mon Sep 04 17:55:01 2017 -0400 @@ -1,4 +1,3 @@ -Gene Counts dme-bantam-3p 11 dme-bantam-5p 0 dme-let-7-3p 0