| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.13 |
| toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.3.1 |
| samtools_fastx |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| samtools | 1.9 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: samtools_fastx-in1.bam output_fmt_cond|output_fmt_select: fasta outputs: other |
attributes: name |
samtools_fastx-in1.bam name |
| Test-2 |
input: samtools_fastx-in2.bam output_fmt_cond|output_fmt_select: fastqsanger outputs: ['r0', 'r1', 'r2'] |
attributes: name attributes: name attributes: name |
samtools_fastx-in2.bam name |
| Test-3 |
input: samtools_fastx-in3.sam output_fmt_cond|output_fmt_select: fasta outputs: ['r0', 'r1', 'r2'] |
attributes: name attributes: name attributes: name |
samtools_fastx-in3.sam name |
| Test-4 |
input: samtools_fastx-in1.bam output_fmt_cond|output_fmt_select: fasta.gz outputs: other |
attributes: name |
samtools_fastx-in1.bam name |
| Test-5 |
input: samtools_fastx-in2.bam output_fmt_cond|output_fmt_select: fastqsanger.gz outputs: ['r0', 'r1', 'r2'] |
attributes: name attributes: name attributes: name |
samtools_fastx-in2.bam name |
| Test-6 |
input: samtools_fastx-in3.sam output_fmt_cond|output_fmt_select: fasta.gz outputs: ['r0', 'r1', 'r2'] |
attributes: name attributes: name attributes: name |
samtools_fastx-in3.sam name |
| Test-7 |
input: bam2fq.001.sam output_fmt_cond|output_fmt_select: fastqsanger outputs: ['r1', 'r2', 'other'] |
attributes: name attributes: name attributes: name |
bam2fq.001.sam name |
| Test-8 |
input: bam2fq.001.sam output_fmt_cond|output_fmt_select: fastqsanger outputs: ['r1', 'r2', 's', 'other'] |
attributes: name attributes: name attributes: name attributes: name |
bam2fq.001.sam name |
| Test-9 |
input: bam2fq.002.sam output_fmt_cond|output_fmt_select: fastqsanger outputs: ['r1', 'r2', 's', 'other'] |
attributes: name attributes: name attributes: name attributes: name |
bam2fq.002.sam name |
| Test-10 |
input: bam2fq.003.sam output_fmt_cond|output_fmt_select: fastqsanger outputs: ['r1', 'r2', 's', 'other'] |
attributes: name attributes: name attributes: name attributes: name |
bam2fq.003.sam name |
| Test-11 |
idxout_cond|write1st: True idxout_cond|idxout_select: yes outputs: ['r1', 'r2', 's', 'other'] idxout_cond|barcode_tag: BC idxout_cond|index_format: n2i2 input: bam2fq.004.sam output_fmt_cond|output_fmt_select: fastqsanger |
attributes: name attributes: name attributes: name attributes: name attributes: name |
bam2fq.004.sam name |
| Test-12 |
idxout_cond|write1st: True output_fmt_cond|output_quality: True outputs: ['r1', 'r2', 's', 'other'] idxout_cond|barcode_tag: BC idxout_cond|index_format: n2i2 input: bam2fq.010.sam output_fmt_cond|output_fmt_select: fastqsanger idxout_cond|idxout_select: yes |
attributes: name attributes: name attributes: name attributes: name attributes: name |
bam2fq.010.sam name |
| Test-13 |
idxout_cond|write1st: True output_fmt_cond|output_quality: True outputs: ['r1', 'r2', 's', 'other'] idxout_cond|barcode_tag: BC idxout_cond|index_format: n2i2 input: bam2fq.010.sam output_fmt_cond|output_fmt_select: fastqsanger idxout_cond|idxout_select: yes |
attributes: name attributes: name attributes: name attributes: name attributes: name |
bam2fq.010.sam name |
| Test-14 |
idxout_cond|write1st: True idxout_cond|idxout_select: yes outputs: ['r1', 'r2', 's', 'other'] read_numbering: -N idxout_cond|barcode_tag: BC idxout_cond|index_format: n*i* input: bam2fq.005.sam output_fmt_cond|output_fmt_select: fastqsanger |
attributes: name attributes: name attributes: name attributes: name attributes: name |
bam2fq.005.sam name |
| Test-15 |
input: bam2fq.005.sam read_numbering: -N copy_tags: True output_fmt_cond|output_fmt_select: fastqsanger outputs: ['r1', 'r2', 's', 'other'] |
attributes: name attributes: name attributes: name attributes: name |
bam2fq.005.sam name |
| Test-16 |
copy_arb_tags: MD,ia outputs: ['r1', 'r2', 's', 'other'] read_numbering: -N input: bam2fq.005.sam copy_tags: True output_fmt_cond|output_fmt_select: fastqsanger |
attributes: name attributes: name attributes: name attributes: name |
bam2fq.005.sam name |
| Test-17 |
copy_arb_tags: MD,ia outputs: ['r1', 'r2', 's', 'other'] read_numbering: -N input: bam2fq.005.sam copy_tags: True output_fmt_cond|output_fmt_select: fastqsanger output_fmt_cond|ilumina_casava: True |
attributes: name attributes: name attributes: name attributes: name |
bam2fq.005.sam name |
| Test-18 |
idxout_cond|write1st: True idxout_cond|idxout_select: yes outputs: ['r1', 'r2', 's', 'other'] idxout_cond|barcode_tag: BC idxout_cond|index_format: n2i2 input: bam2fq.004.sam output_fmt_cond|output_fmt_select: fastqsanger output_fmt_cond|ilumina_casava: True |
attributes: name attributes: name attributes: name attributes: name attributes: name |
bam2fq.004.sam name |