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authorCalvin Morrison <mutantturkey@gmail.com>2014-09-09 17:53:01 -0400
committerCalvin Morrison <mutantturkey@gmail.com>2014-09-09 17:53:01 -0400
commita9b3d721ac6057a84377cdeedafa986f7cf35b95 (patch)
tree9b3b3fced96978edafa1c2ebbc0a912539009495
parent3f3633d36cb033da5a7d616463a32397bd77c478 (diff)
parent62067f0ca6db19fcdedc84476e68ba3864062f54 (diff)
Merge branch 'master' of github.com:EESI/quikrHEADmaster
-rw-r--r--src/c/quikr_train.c10
-rw-r--r--src/galaxy/multifasta2otu.xml6
-rw-r--r--src/galaxy/quikr.xml20
-rw-r--r--src/galaxy/quikr_train.xml18
4 files changed, 12 insertions, 42 deletions
diff --git a/src/c/quikr_train.c b/src/c/quikr_train.c
index 08a1f0a..1260b86 100644
--- a/src/c/quikr_train.c
+++ b/src/c/quikr_train.c
@@ -34,7 +34,7 @@ int main(int argc, char **argv) {
unsigned long long position = 0;
int verbose = 0;
-
+ int force_name = 0;
char *fasta_filename = NULL;
char *output_file = NULL;
@@ -45,6 +45,7 @@ int main(int argc, char **argv) {
while (1) {
static struct option long_options[] = {
{"verbose", no_argument, 0, 'v'},
+ {"force_name", no_argument, 0, 'f'},
{"help", no_argument, 0, 'h'},
{"version", no_argument, 0, 'V'},
{"input", required_argument, 0, 'i'},
@@ -55,7 +56,7 @@ int main(int argc, char **argv) {
int option_index = 0;
- c = getopt_long (argc, argv, "i:o:k:hvV", long_options, &option_index);
+ c = getopt_long (argc, argv, "i:o:k:fhvV", long_options, &option_index);
if (c == -1)
break;
@@ -73,6 +74,9 @@ int main(int argc, char **argv) {
case 'v':
verbose = 1;
break;
+ case 'f':
+ force_name = 1;
+ break;
case 'V':
printf("%s\n", VERSION);
exit(EXIT_SUCCESS);
@@ -117,7 +121,7 @@ int main(int argc, char **argv) {
exit(EXIT_FAILURE);
}
- if(strcmp(&output_file[strlen(output_file) - 3], ".gz") != 0) {
+ if(strcmp(&output_file[strlen(output_file) - 3], ".gz") != 0 && !force_name) {
char *temp = malloc(strlen(output_file) + 4);
if(temp == NULL) {
fprintf(stderr, "Could not allocate enough memory\n");
diff --git a/src/galaxy/multifasta2otu.xml b/src/galaxy/multifasta2otu.xml
index b80f8b2..eebe246 100644
--- a/src/galaxy/multifasta2otu.xml
+++ b/src/galaxy/multifasta2otu.xml
@@ -1,10 +1,10 @@
<tool id="multifasta" name="Multifasta">
<description>Get Abundances on Multiple Files</description>
- <command interpreter="bash">multifasta_to_otu -k $kmer -s $db -f &lt;( echo
+ <command>bash -c "multifasta_to_otu -k $kmer -s $db -f &lt;( echo
#for $input in $inputs:
-"${input}"
+${input}
#end for
- | xargs -n 1 ) -o $output</command>
+ | xargs -n 1 ) -o $output"</command>
<inputs>
<param name="inputs" multiple="true" type="data" format="fasta" label="input fasta"/>
<param name="db" type="data" format="data" label="trained database"/>
diff --git a/src/galaxy/quikr.xml b/src/galaxy/quikr.xml
index 89729be..65d604b 100644
--- a/src/galaxy/quikr.xml
+++ b/src/galaxy/quikr.xml
@@ -11,23 +11,7 @@
<data name="output" format="tabular"/>
</outputs>
<help>
-**What it does**
-
-This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
-
------
-
-**Example**
-
-Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
-
- &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
-
-Running this tool while setting **How many characters to keep?** to **14** will produce this::
-
- EYKX4VC02EQLO5 108
- EYKX4VC02D4GS2 60
-
-
</help>
</tool>
+
+
diff --git a/src/galaxy/quikr_train.xml b/src/galaxy/quikr_train.xml
index b5f5291..a33d866 100644
--- a/src/galaxy/quikr_train.xml
+++ b/src/galaxy/quikr_train.xml
@@ -9,23 +9,5 @@
<data name="output" format="data"/>
</outputs>
<help>
-**What it does**
-
-This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
-
------
-
-**Example**
-
-Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
-
- &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
-
-Running this tool while setting **How many characters to keep?** to **14** will produce this::
-
- EYKX4VC02EQLO5 108
- EYKX4VC02D4GS2 60
-
-
</help>
</tool>