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Commit message:
planemo upload for repository www.github.com |
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added:
2.fasta 2.fastq seqtk_seq.xml test-data/2.fasta test-data/2.fastq |
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| diff -r 000000000000 -r 7f1d97518adc 2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/2.fasta Wed Apr 11 19:46:44 2018 -0400 |
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| @@ -0,0 +1,6 @@ +>EAS54_6_R1_2_1_413_324 +CCCTTCTTGTCTTCAGCGTTTCTCC +>EAS54_6_R1_2_1_540_792 +TTGGCAGGCCAAGGCCGATGGATCA +>EAS54_6_R1_2_1_443_348 +GTTGCTTCTGGCGTGGGTGGGGGGG |
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| diff -r 000000000000 -r 7f1d97518adc 2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/2.fastq Wed Apr 11 19:46:44 2018 -0400 |
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| @@ -0,0 +1,12 @@ +@EAS54_6_R1_2_1_413_324 +CCCTTCTTGTCTTCAGCGTTTCTCC ++ +;;3;;;;;;;;;;;;7;;;;;;;88 +@EAS54_6_R1_2_1_540_792 +TTGGCAGGCCAAGGCCGATGGATCA ++ +;;;;;;;;;;;7;;;;;-;;;3;83 +@EAS54_6_R1_2_1_443_348 +GTTGCTTCTGGCGTGGGTGGGGGGG ++EAS54_6_R1_2_1_443_348 +;;;;;;;;;;;9;7;;.7;393333 \ No newline at end of file |
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| diff -r 000000000000 -r 7f1d97518adc seqtk_seq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_seq.xml Wed Apr 11 19:46:44 2018 -0400 |
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| @@ -0,0 +1,57 @@ +<tool id="seqtk_seq" name="Convert to FASTA (seqtk)" version="0.1.0"> + <requirements> + <requirement type="package" version="1.2">seqtk</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + seqtk seq -a "$input1" > "$output1" + ]]></command> + <inputs> + <param type="data" name="input1" format="fastq" /> + </inputs> + <outputs> + <data name="output1" format="fasta" /> + </outputs> + <tests> + <test> + <param name="input1" value="2.fastq"/> + <output name="output1" file="2.fasta"/> + </test> + </tests> + <help><![CDATA[ + +Usage: seqtk seq [options] <in.fq>|<in.fa> + +Options: -q INT mask bases with quality lower than INT [0] + -X INT mask bases with quality higher than INT [255] + -n CHAR masked bases converted to CHAR; 0 for lowercase [0] + -l INT number of residues per line; 0 for 2^32-1 [0] + -Q INT quality shift: ASCII-INT gives base quality [33] + -s INT random seed (effective with -f) [11] + -f FLOAT sample FLOAT fraction of sequences [1] + -M FILE mask regions in BED or name list FILE [null] + -L INT drop sequences with length shorter than INT [0] + -c mask complement region (effective with -M) + -r reverse complement + -A force FASTA output (discard quality) + -C drop comments at the header lines + -N drop sequences containing ambiguous bases + -1 output the 2n-1 reads only + -2 output the 2n reads only + -V shift quality by '(-Q) - 33' + -U convert all bases to uppercases + -S strip of white spaces in sequences + + + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubseqtk, + author = {LastTODO, FirstTODO}, + year = {TODO}, + title = {seqtk}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/lh3/seqtk}, +}</citation> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 7f1d97518adc test-data/2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.fasta Wed Apr 11 19:46:44 2018 -0400 |
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| @@ -0,0 +1,6 @@ +>EAS54_6_R1_2_1_413_324 +CCCTTCTTGTCTTCAGCGTTTCTCC +>EAS54_6_R1_2_1_540_792 +TTGGCAGGCCAAGGCCGATGGATCA +>EAS54_6_R1_2_1_443_348 +GTTGCTTCTGGCGTGGGTGGGGGGG |
| b |
| diff -r 000000000000 -r 7f1d97518adc test-data/2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.fastq Wed Apr 11 19:46:44 2018 -0400 |
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| @@ -0,0 +1,12 @@ +@EAS54_6_R1_2_1_413_324 +CCCTTCTTGTCTTCAGCGTTTCTCC ++ +;;3;;;;;;;;;;;;7;;;;;;;88 +@EAS54_6_R1_2_1_540_792 +TTGGCAGGCCAAGGCCGATGGATCA ++ +;;;;;;;;;;;7;;;;;-;;;3;83 +@EAS54_6_R1_2_1_443_348 +GTTGCTTCTGGCGTGGGTGGGGGGG ++EAS54_6_R1_2_1_443_348 +;;;;;;;;;;;9;7;;.7;393333 \ No newline at end of file |