add help.txt

src/kallisto/kallisto_quant/help.txt

@@ -0,0 +1,33 @@
+```
+kallisto quant
+```
+
+kallisto 0.50.1
+Computes equivalence classes for reads and quantifies abundances
+
+Usage: kallisto quant [arguments] FASTQ-files
+
+Required arguments:
+-i, --index=STRING            Filename for the kallisto index to be used for
+                              quantification
+-o, --output-dir=STRING       Directory to write output to
+
+Optional arguments:
+-b, --bootstrap-samples=INT   Number of bootstrap samples (default: 0)
+    --seed=INT                Seed for the bootstrap sampling (default: 42)
+    --plaintext               Output plaintext instead of HDF5
+    --single                  Quantify single-end reads
+    --single-overhang         Include reads where unobserved rest of fragment is
+                              predicted to lie outside a transcript
+    --fr-stranded             Strand specific reads, first read forward
+    --rf-stranded             Strand specific reads, first read reverse
+-l, --fragment-length=DOUBLE  Estimated average fragment length
+-s, --sd=DOUBLE               Estimated standard deviation of fragment length
+                              (default: -l, -s values are estimated from paired
+                               end data, but are required when using --single)
+-p, --priors                  Priors for the EM algorithm, either as raw counts or as
+                              probabilities. Pseudocounts are added to raw reads to
+                              prevent zero valued priors. Supplied in the same order
+                              as the transcripts in the transcriptome
+-t, --threads=INT             Number of threads to use (default: 1)
+    --verbose                 Print out progress information every 1M proccessed reads