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Type: align-reads-with-bowtie
| output-dir | Output directory | string |
| reference | Reference genome | string |
| outname | Output file name | string |
| mismatches_type | Mode | numericstring |
| mismatches_number | Mismatches number | numeric |
| maqerr | Mismatches number | numeric |
| seedLen | Seed length | numeric |
| maxbts | Maximum of backtracks | numeric |
| chunkmbs | Best hits | numeric |
| seed | Seed | numeric |
| colorspace | Colorspace | numericboolean |
| nomaqround | No Maq rounding | boolean |
| nofw | No forward orientation | boolean |
| norc | No reverse-complement orientation | numericboolean |
| tryhard | Try as hard | numericboolean |
| best | Best alignments | numericboolean |
| all | All alignment | numericboolean |
Parameter | Parameter in the GUI | Type |
|---|
static const QString IN_TYPE_ID("Bowtie-data");
static const QString OUT_TYPE_ID("Bowtie-data-out");
static const QString ASSEBLY_OUT_SLOT_ID("assembly-out");
static const QString OUT_PORT_DESCR("out-data");static const QString MISMATCHES_TYPE = "mismatches_type";
static const QString MISMATCHES_NUMBER = "mismatches_number";static const QString MAQERR = "maqerr";
static const QString CHUNKMBS = "chunkmbs";
static const QString BASE_Bowtie_SUBDIR("bowtie");
static const QString BASE_Bowtie_OUTFILE("out.sam");
Input/Output Ports
The element has 1 input port:
Name in GUI: Bowtie data
Name in Workflow File: in-data
Slots:
| URL of a file with mate reads | readsurl | string |
| URL of a file with reads | readspairedurl | string |
Slot In GUI | Slot in Workflow File | Type |
|---|
And 1 output port:
Name in GUI: BWA-MEM Bowtie output data
Name in Workflow File: out-data
Slots:
Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Assembly URL | assembly-out | string |