| Previous changeset 26:7d80b2b24270 (2015-03-30) Next changeset 28:fdc981664a43 (2015-04-01) |
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Commit message:
Add bam-dump and test data. |
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modified:
fastq_dump.xml |
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added:
bam_dump.xml test-data/fastq_dump_result.fastq |
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| diff -r 7d80b2b24270 -r 8be4f23d1018 bam_dump.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bam_dump.xml Mon Mar 30 22:40:59 2015 -0400 |
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| @@ -0,0 +1,88 @@ +<tool id="bam_dump" name="Extract reads" version="1.1.2"> + <description> in BAM format from NCBI SRA.</description> + <command> + sam-dump --log-level fatal + #if str( $region ) != "": + --aligned-region $region + #end if + #if str( $matepairDist ) != "": + --matepair-distance $matepairDist + #end if + #if str( $minMapq ) != "": + --minmapq $minMapq + #end if + #if $header == "yes": + --header + #else: + --no-header + #end if + #if str( $alignments ) == "both": + --unaligned + #end if + #if str( $alignments ) == "unaligned": + --unaligned-spots-only + #end if + #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ): + --primary + #end if + #if $input.input_select == "file": + $input.file + #elif $input.input_select == "accession_number": + $input.accession + #elif $input.input_select == "text": + `cat $input.text` + #end if + | samtools view -Sb - > $output + </command> + <version_string>sam-dump --version</version_string> + <inputs> + <conditional name="input"> + <param name="input_select" type="select" label="select input type"> + <option value="accession_number">SRR accession</option> + <option value="file">SRA archive in current history</option> + <option value="text">text file containing SRR accession</option> + </param> + <when value="file"> + <param format="sra" name="file" type="data" label="sra archive"/> + </when> + <when value="accession_number"> + <param format="text" name="accession" type="text" label="accession"/> + </when> + <when value="text"> + <param format="txt" name="text" type="data" label="text file"/> + </when> + </conditional> + <param format="text" name="region" type="text" label="aligned region"/> + <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/> + <param format="text" name="header" type="select" value="yes"> + <label>output BAM header</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param format="text" name="alignments" type="select" value="both"> + <label>aligned or unaligned reads</label> + <option value="both">both</option> + <option value="aligned">aligned only</option> + <option value="unaligned">unaligned only</option> + </param> + <param format="text" name="primary" type="select" value="no"> + <label>only primary aligments</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> + </inputs> + <outputs> + <data name="output" format="bam"/> + </outputs> + <requirements> + <requirement type="package" version="2.4.5">sra_toolkit</requirement> + <requirement type="package" version="1.2">samtools</requirement> + </requirements> + <help> + This tool extracts reads from sra archives using sam-dump. + Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. + The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. + Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. + </help> +</tool> |
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| diff -r 7d80b2b24270 -r 8be4f23d1018 fastq_dump.xml --- a/fastq_dump.xml Mon Mar 30 22:11:38 2015 -0400 +++ b/fastq_dump.xml Mon Mar 30 22:40:59 2015 -0400 |
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| @@ -114,6 +114,14 @@ <requirements> <requirement type="package" version="2.4.5">sra_toolkit</requirement> </requirements> + <tests> + <test> + <param name="input_select" value="accession_number"/> + <param name="accession" value="SRR000001"/> + <param name="maxID" value="5"/> + <output name="output" file="fastq_dump_result.fastq" ftype="fastq" /> + </test> + </tests> <help> This tool extracts reads from SRA archives using fastq-dump. Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. |
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| diff -r 7d80b2b24270 -r 8be4f23d1018 test-data/fastq_dump_result.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dump_result.fastq Mon Mar 30 22:40:59 2015 -0400 |
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| @@ -0,0 +1,80 @@ +@EM7LVYS01C1LWG_Adapter/1 +TCAG ++SRR000001.1 EM7LVYS01C1LWG length=4 +=;8G +@EM7LVYS01C1LWG_Mate1/2 +GGGGGAGCTTAAATTTGAAACTAGAAAAATTTTGAACAAAATAATCATAATTGTTAGCTGATGAAAAACTAGAAAAGATTTTCTGAGT ++SRR000001.1 EM7LVYS01C1LWG length=88 +C91*#==<C=EA.EA/<B=(<<:=HC90'FB5&;B:<GC6(=D=<<==C=C==B<=<<<=;<<GC8.#<<9=FB4%<8EA4%87:<<8 +@EM7LVYS01C1LWG_Linker/3 +GTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAAC ++SRR000001.1 EM7LVYS01C1LWG length=44 +=B;C<@8>5=C?*A<&A<&<=49/2A='@;#A<&<A9C=@9B:: +@EM7LVYS01C1LWG_Mate2/4 +GGTATCCCGTAGTGTGCATTCATCCCTGCTCTGGATACAGTCAGCTCCCAAATTCCATAAACAACTCCTTTGTAAGTAACCTCCTTTTGACAGGGGGTACTGAGCGGGCTGGCAAGGCN ++SRR000001.1 EM7LVYS01C1LWG length=119 +B:<;=C?+<<;<===<=;C<==<FB0=<=<<<D=9=;;=<=<=<;=FB2FB2C<C<;=FB0<C==;C<D@-<=B:<=C=C;<C=GD7*=;:=HD90'==<<=<=:FB0<<C<;C=C=<! +@EM7LVYS01B2EMP_Adapter/1 +TCAG ++SRR000001.2 EM7LVYS01B2EMP length=4 +=<8F +@EM7LVYS01B2EMP_Mate1/2 +GGGGGGGTTACACGTGCAGATTTGTTACACGGGTGTACTGTGAGGTTTGGGGTACGAATGATCCCGTTACCTAGATAGTGAGCATGGAACCC ++SRR000001.2 EM7LVYS01B2EMP length=92 +@71-*&#D=<=<=<===<<:FB1=C=;<=<FA/==<<=<===<D=FB0FB4%<<=<B;=;;;FB2=D=<C<=;=<;<==<==<:;D=C=FB1 +@EM7LVYS01B2EMP_Linker/3 +GTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAAC ++SRR000001.2 EM7LVYS01B2EMP length=44 +<C<>6=4>5:@<%@;$@<%=<3;1:D@,D@-A='=C=D=B:C<7 +@EM7LVYS01B2EMP_Mate2/4 +AATGTGCAGGGCTCAGGTCAGCATTAGGGTCAGGTTCTTAGGAAAAGAAAGAGCAAAAACAATGAAACACAATACAAAGTAAAGAACACTGAGCGGGCTGGCAAGGCN ++SRR000001.2 EM7LVYS01B2EMP length=108 +9.<===;;EA.<<<<C;;===<;C=<FB1<;=C=C<<C==D=GC6)<?;"<=<=HC9/%;B;==FB0<<<C<=<;FB2<;B=(8D=<:<98<;=EA/=<A9;C;>6=! +@EM7LVYS01C2YO0_Adapter/1 +TCAG ++SRR000001.3 EM7LVYS01C2YO0 length=4 +<==G +@EM7LVYS01C2YO0_Mate1/2 +GGGGGGAGATACATCCTTTTCAAGAAGACGTAGAACATTTATTAAAATTGACCACATGCTGAGATACACCGAGAAACTCTCAAATTTGGAAGGACTGAAATCATACAAAGTACGTTTTCTTACTACAATGCAATTAAGTTGGAAATCAAATAGCAAAAATAAAATAAAAACTATTTATAT ++SRR000001.3 EM7LVYS01C2YO0 length=180 +A82-)$6==8:::<B;FB5&=C==C<<<<==<<C;<<FB/:C<EA3#@8;=C;:=<<<===<;<;;=<C<<<;FB0<;<<<EA/FB/C<C=@83;<<FB07=<<<<D@,8=;<=GC6)<B:<<<=;A9<=;C;C<<3:B:C<E@-==EA.=98<HD90&=HD8+4GC8-"2;5FB19<43 +@EM7LVYS01C2YO0_Linker/3 +GTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAAC ++SRR000001.3 EM7LVYS01C2YO0 length=44 +9C=D=B;B<<FB1D?+FB0=C<B;<FB1FB1D@,<B<B<C<C=< +@EM7LVYS01C2YO0_Mate2/4 +TTAAACTTAAAAAAATTTTTTCTAGTTATTTTATTTTGTTTGAAACAGAAATCAACTGAGCGGGCTGGCAAGGCNNNNN ++SRR000001.3 EM7LVYS01C2YO0 length=79 +C=FB1<C<GB82-(#GB92,';(5:9.=FB4%8GC8,:FB0<D?+=<5?;"7:=46868;8D?+:<@8=D==59!!!!! +@EM7LVYS01CD8YZ_Adapter/1 +TCAG ++SRR000001.4 EM7LVYS01CD8YZ length=4 +=<:< +@EM7LVYS01CD8YZ_Mate1/2 +ATCATTACAGACGGAACAGAAATAACTCAGGCAAGCCAGCTGCAACGAGAGGCAGGGCCCAGCGACAGCGCCTGGGTGGGCCTGG ++SRR000001.4 EM7LVYS01CD8YZ length=85 +<<<=C=<=<<<=C;?6=<<FB2<B;;<<=A9=?7<B:<<=<<<>6=<=<=A:<=C?*C?*=;=<<<<<==C<<B=(;EA2A9<D@ +@EM7LVYS01CD8YZ_Linker/3 +GTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAAC ++SRR000001.4 EM7LVYS01CD8YZ length=44 +,C<@8;2?6<A<&B=(C?+=>6A:8C?+@;$C?*=D=C=B:@8B +@EM7LVYS01CD8YZ_Mate2/4 +CAGGAGGTCGAGGTTGCAGTGAGCCAAATCATGCTACTGTACAGTCTGGGTGACAGAGTGAGACCCTGTCTGAGCGGGCTGGCAAGGCN ++SRR000001.4 EM7LVYS01CD8YZ length=89 +:=C==>6;=<<A9?7==;=<=<;B;EA2==<<=<=<<8:<=<7;==8D@,<<=<;<<==<=<<E@-=;7<<<<7;C?*6<C<<C<C<<! +@EM7LVYS01CB53W_Adapter/1 +TCAG ++SRR000001.5 EM7LVYS01CB53W length=4 +<=<H +@EM7LVYS01CB53W_Mate1/2 +GGGGGCG ++SRR000001.5 EM7LVYS01CB53W length=7 +C92+%8B +@EM7LVYS01CB53W_Linker/3 +GTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAAC ++SRR000001.5 EM7LVYS01CB53W length=44 +:?7A9@7>6=D@-EA.C?*<A9?66D@,B>)B=(<@8D=C=>5= +@EM7LVYS01CB53W_Mate2/4 +AGCCTCAAGGGCCAAAGAATGGTGTTCTCAAACTGCCATGCCACAGGACAAACTGAGCTCGCTGAGGGGACAGGAGAAGAAACGTGGGGCCATGAGGTCTCCTGAGCGGGCTGGCAAGGC ++SRR000001.5 EM7LVYS01CB53W length=120 +<<A9<<B;EA.C<C>*;C=;C<=9A::<:FB0<<=B;=<;C<<;;D=8<FB0<=<=<<=8;;=:=HD8,=<<A<:<A9;FB0<:=GC6(B;;:<=D=9=<C<=:=3=EA.==D=<@7C;: |