diff options
| author | Calvin Morrison <mutantturkey@gmail.com> | 2014-06-19 16:24:16 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2014-06-19 16:24:16 -0400 |
| commit | f254e4b8959cf9b0f1e93a7dccdb492e1166c975 (patch) | |
| tree | 31253a1547450ec663a9c812d735bc7c49ae9ddf | |
| parent | 5c1fa49a88351cb64b952bfeb1ac6873691ce8ea (diff) | |
galaxy XML
| -rw-r--r-- | galaxy/kmer_counts_per_sequence.xml | 32 | ||||
| -rw-r--r-- | galaxy/kmer_total_count.xml | 32 |
2 files changed, 64 insertions, 0 deletions
diff --git a/galaxy/kmer_counts_per_sequence.xml b/galaxy/kmer_counts_per_sequence.xml new file mode 100644 index 0000000..c1ef57f --- /dev/null +++ b/galaxy/kmer_counts_per_sequence.xml @@ -0,0 +1,32 @@ +<tool id="countspersequence" name="Kmer Counts Per Sequence"> + <description>get kmer counts for each sequence</description> + <command> + kmer_counts_per_sequence + -k $kmer + #if labels: + -l + #endif + #if $reverse: + -c + #endif + #if $sparse: + -s + #endif + -i $input > $output + </command> + <inputs> + <param name="input" type="data" format="fasta" label="input fasta file"/> + <param name="kmer" type="integer" size="2" value="6" label="What mer size to use?" help="range 1 - 30"/> + <param name="labels" type="boolean" value="True" label="do you want mer labels (AAA, AAC, AAG) shown?" help="" /> + <param name="reverse" type="boolean" value="True" label="do you want to count both strands (the reverse compliment)?" help="" /> + <param name="sparse" type="boolean" value="True" label="do you want to output only nonzero counts?"help="" /> + </inputs> + <outputs> + <data name="output" format="tabular"/> + </outputs> + <help> + input a sample file, get a count of kmers in each sequence + </help> +</tool> + + diff --git a/galaxy/kmer_total_count.xml b/galaxy/kmer_total_count.xml new file mode 100644 index 0000000..05c3b10 --- /dev/null +++ b/galaxy/kmer_total_count.xml @@ -0,0 +1,32 @@ +<tool id="total_count" name="Kmer Total Count"> + <description>count kmers in a samlpe</description> + <command> + kmer_total_count + -k $kmer + #if labels: + -l + #endif + #if $reverse + -c + #endif + #if $sparse: + -n + #endif + -i $input > $output + </command> + <inputs> + <param name="input" type="data" format="fasta" label="input fasta file"/> + <param name="kmer" type="integer" size="2" value="6" label="What mer size to use?" help="range 1 - 30"/> + <param name="labels" type="boolean" value="True" label="do you want mer labels (AAA, AAC, AAG) shown?" help="" /> + <param name="reverse" type="boolean" value="True" label="do you want to count both strands (the reverse compliment)?" help="" /> + <param name="sparse" type="boolean" value="True" label="do you want to output only nonzero counts?"help="" /> + </inputs> + <outputs> + <data name="output" format="tabular"/> + </outputs> + <help> + input a sample file, get a count of kmers in each sequence + </help> +</tool> + + |