comparison test-data/make_test_data.sh @ 0:b4098353ee73 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
author galaxyp
date Fri, 05 Jan 2018 12:47:36 -0500
parents
children 8f0e76ad46ef
comparison
equal deleted inserted replaced
-1:000000000000 0:b4098353ee73
1 #!/bin/bash
2
3 #must be run within tools-galaxyp/tools/moFF/test-data
4
5 conda create -n mofftestdata moff
6 source activate mofftestdata
7
8 moff_all.py --inputtsv input/mbr_test1.tabular input/mbr_test2.tabular \
9 --inputraw input/mbr_test1.mzml input/mbr_test2.mzml \
10 --tol 10 \
11 --rt_w 3 \
12 --rt_p 1 \
13 --rt_p_match 1.2 \
14 --peptide_summary 1 \
15 --output_folder output1
16
17 moff.py --inputtsv input/test.tabular \
18 --inputraw input/test.mzml \
19 --tol 10 \
20 --rt_w 3 \
21 --rt_p 1 \
22 --rt_p_match 1.2 \
23 --peptide_summary 1 \
24 --output_folder output2
25 mv output2/peptide_summary_intensity_moFF_run.tab output2/moff_test_pepsum.tab
26
27 moff_mbr.py \
28 --inputF input \
29 --ext tabular \
30 --sample mbr_*
31
32
33 # clean up
34 # mbr outputs for moff all
35 rm -r output1/mbr_output
36
37 # logs
38 rm output1/*.log output2/*.log
39
40 # peptide summary for all
41 rm output1/peptide_summary_intensity_moFF_run.tab