Mercurial > repos > lparsons > htseq_count
comparison htseq-count.xml @ 25:88cea300225a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212
| author | iuc |
|---|---|
| date | Tue, 17 Jan 2017 09:26:25 -0500 |
| parents | 0c01ed8d0e60 |
| children | d8c5761a8ba7 |
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| 24:0c01ed8d0e60 | 25:88cea300225a |
|---|---|
| 1 <tool id="htseq_count" name="htseq-count" version="0.6.1galaxy2" profile="16.04"> | 1 <tool id="htseq_count" name="htseq-count" version="0.6.1galaxy3" profile="16.04"> |
| 2 <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description> | 2 <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.6.1.post1">htseq</requirement> | 4 <requirement type="package" version="0.6.1.post1">htseq</requirement> |
| 5 <requirement type="package" version="0.1.19">samtools</requirement> | 5 <requirement type="package" version="1.3.1">samtools</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 | 7 |
| 8 <stdio> | 8 <stdio> |
| 9 <exit_code range="1:" level="fatal" description="Unknown error occurred" /> | 9 <exit_code range="1:" level="fatal" description="Unknown error occurred" /> |
| 10 <regex match="htseq-count: (command ){0,1}not found" source="stderr" level="fatal" description="The HTSeq python package is not properly installed, contact Galaxy administrators" /> | 10 <regex match="htseq-count: (command ){0,1}not found" source="stderr" level="fatal" description="The HTSeq python package is not properly installed, contact Galaxy administrators" /> |
| 21 ##set up input files | 21 ##set up input files |
| 22 #set $reference_fasta_filename = "localref.fa" | 22 #set $reference_fasta_filename = "localref.fa" |
| 23 #if $samout_conditional.samout == "Yes": | 23 #if $samout_conditional.samout == "Yes": |
| 24 #if str( $samout_conditional.reference_source.reference_source_selector ) == "history": | 24 #if str( $samout_conditional.reference_source.reference_source_selector ) == "history": |
| 25 ln -s "${samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" && | 25 ln -s "${samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" && |
| 26 samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 && | 26 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 && |
| 27 #else: | 27 #else: |
| 28 #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path ) | 28 #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path ) |
| 29 #end if | 29 #end if |
| 30 #end if | 30 #end if |
| 31 | 31 |
| 32 #if $force_sort == "True": | 32 #if $force_sort == "True": |
| 33 #if $samfile.extension == 'bam': | 33 #if $samfile.extension == 'bam': |
| 34 samtools sort -n "$samfile" "name_sorted_alignment" && | 34 samtools sort -n -o 'name_sorted_alignment.bam' '$samfile' && |
| 35 #else | 35 #else |
| 36 samtools view -Su -t "${reference_fasta_filename}.fai" "$samfile" | samtools sort -n - "name_sorted_alignment" && | 36 samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' | samtools sort -n -o 'name_sorted_alignment.bam' - && |
| 37 #end if | 37 #end if |
| 38 #end if | 38 #end if |
| 39 | 39 |
| 40 htseq-count | 40 htseq-count |
| 41 --mode=$mode | 41 --mode=$mode |
| 42 --stranded=$stranded | 42 --stranded=$stranded |
| 43 --minaqual=$minaqual | 43 --minaqual=$minaqual |
| 44 --type="$featuretype" | 44 --type='$featuretype' |
| 45 --idattr="$idattr" | 45 --idattr='$idattr' |
| 46 #if $samout_conditional.samout == "Yes": | 46 #if $samout_conditional.samout == "Yes": |
| 47 --samout='$__new_file_path__/${samoutfile.id}_tmp' | 47 --samout='$__new_file_path__/${samoutfile.id}_tmp' |
| 48 #end if | 48 #end if |
| 49 #if $force_sort == "True": | 49 #if $force_sort == "True": |
| 50 --order=name | 50 --order=name |
| 53 #else | 53 #else |
| 54 --order=pos | 54 --order=pos |
| 55 --format=$samfile.extension | 55 --format=$samfile.extension |
| 56 '$samfile' | 56 '$samfile' |
| 57 #end if | 57 #end if |
| 58 | 58 |
| 59 "$gfffile" | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&2"; else print $0}' | 59 "$gfffile" | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&2"; else print $0}' |
| 60 > '$counts' | 60 > '$counts' |
| 61 2> '$othercounts' | 61 2> '$othercounts' |
| 62 | 62 |
| 63 #if $samout_conditional.samout == "Yes": | 63 #if $samout_conditional.samout == "Yes": |
| 64 && samtools view -Su | 64 && samtools view -Su |
| 65 -t "${reference_fasta_filename}.fai" | 65 -t '${reference_fasta_filename}.fai' |
| 66 "$__new_file_path__/${samoutfile.id}_tmp" | 66 '$__new_file_path__/${samoutfile.id}_tmp' |
| 67 | samtools sort -o - name_sorted_alignment > "$samoutfile" | 67 | samtools sort -o '$samoutfile' - |
| 68 #end if | 68 #end if |
| 69 ]]> | 69 ]]> |
| 70 </command> | 70 </command> |
| 71 | 71 |
| 72 <inputs> | 72 <inputs> |
| 177 <param name="samout" value="No" /> | 177 <param name="samout" value="No" /> |
| 178 <param name="force_sort" value="True" /> | 178 <param name="force_sort" value="True" /> |
| 179 <output name="counts" file="htseq-test-paired_counts.tsv" /> | 179 <output name="counts" file="htseq-test-paired_counts.tsv" /> |
| 180 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" /> | 180 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" /> |
| 181 </test> | 181 </test> |
| 182 | |
| 183 <test> | 182 <test> |
| 184 <param name="samfile" value="htseq-test.sam" /> | 183 <param name="samfile" value="htseq-test.sam" /> |
| 185 <param name="gfffile" value="htseq-test.gff" /> | 184 <param name="gfffile" value="htseq-test.gff" /> |
| 186 <param name="samout" value="Yes" /> | 185 <param name="samout" value="Yes" /> |
| 187 <param name="reference_source_selector" value="history" /> | 186 <param name="reference_source_selector" value="history" /> |
| 283 Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology | 282 Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology |
| 284 Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General | 283 Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General |
| 285 Public License v3. Part of the 'HTSeq' framework. | 284 Public License v3. Part of the 'HTSeq' framework. |
| 286 ]]> | 285 ]]> |
| 287 </help> | 286 </help> |
| 288 | |
| 289 <citations> | 287 <citations> |
| 290 <citation type="doi">10.1093/bioinformatics/btu638</citation> | 288 <citation type="doi">10.1093/bioinformatics/btu638</citation> |
| 291 </citations> | 289 </citations> |
| 292 </tool> | 290 </tool> |