Mercurial > repos > crusoe > khmer
annotate count-median.xml @ 48:bcd19db01a6b
fix filter-abund file name
| author | Michael R. Crusoe <mcrusoe@msu.edu> |
|---|---|
| date | Sat, 12 Jul 2014 15:18:24 -0400 |
| parents | 0b238b083f77 |
| children | bbfc8bf96469 |
| rev | line source |
|---|---|
| 14 | 1 <tool id="gedlab-khmer-count-median" |
| 10 | 2 name="Count Median" |
| 3 version="1.1-1" | |
| 4 force_history_refresh="true"> | |
| 5 | |
| 6 <description> | |
| 7 Count the median/avg k-mer abundance for each sequence in the input file, | |
| 8 based on the k-mer counts in the given k-mer counting table. Can be used to | |
| 9 estimate expression levels (mRNAseq) or coverage (genomic/metagenomic). | |
| 10 </description> | |
| 11 <macros> | |
|
11
cec78b574760
Actually import the macros
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
10
diff
changeset
|
12 <token name="@BINARY@">count-median.py</token> |
|
cec78b574760
Actually import the macros
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
10
diff
changeset
|
13 <import>macros.xml</import> |
| 10 | 14 </macros> |
| 15 <expand macro="requirements" /> | |
| 16 <command> | |
| 17 ## The command is a Cheetah template which allows some Python based syntax. | |
| 18 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces | |
| 19 mkdir output; cd output; | |
| 20 @BINARY@ | |
| 21 $input_counting_table_filename | |
| 22 $input_sequence_filename | |
| 23 $output_summary_filename | |
| 24 </command> | |
| 25 | |
| 26 <inputs> | |
| 27 <expand macro="input_sequence_filename" /> | |
| 28 <expand macro="input_counting_table_filename" /> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data name="output_summary_filename" format="text" label="${input_sequence_filename} sequence id, median, average, stddev, and seq length" /> | |
| 32 </outputs> | |
| 33 <stdio> | |
| 34 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
| 35 <exit_code range="1:" | |
| 36 level="fatal" /> | |
| 37 </stdio> | |
| 28 | 38 |
| 39 <tests> | |
| 45 | 40 <test interactor="api"> |
| 28 | 41 <param name="input_sequence_filename" value="test-abund-read-2.fa" /> |
| 34 | 42 <param name="input_counting_table_filename" value="test-abund-read-2.ct" ftype="ct" /> |
| 28 | 43 <output name="output_summary_filename"> |
| 44 <assert_contents> | |
|
33
d067ee282412
Switch line matching, api specification
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
28
diff
changeset
|
45 <has_line_matching expression="seq 1001 1001.0 0.0 18" /> |
|
d067ee282412
Switch line matching, api specification
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
28
diff
changeset
|
46 <has_line_matching expression="895:1:37:17593:9954/1 1 103.803741455 303.702941895 114" /> |
| 28 | 47 </assert_contents> |
| 48 </output> | |
| 49 </test> | |
| 50 </tests> | |
| 10 | 51 |
| 52 <!-- [OPTIONAL] Help displayed in Galaxy --> | |
| 53 <!-- | |
| 54 <help> | |
| 55 </help> | |
| 56 --> | |
| 57 </tool> |