Mercurial > repos > galaxyp > proteomics_moff

comparison test-data/make_test_data.sh @ 1:8f0e76ad46ef draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41
author galaxyp
date Thu, 18 Jan 2018 00:51:56 -0500
parents b4098353ee73
children
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0:b4098353ee73 1:8f0e76ad46ef
1 #!/bin/bash 1 #!/bin/bash
2 2
3 #must be run within tools-galaxyp/tools/moFF/test-data 3 #must be run within tools-galaxyp/tools/moFF/test-data
4 4
5 conda create -n mofftestdata moff 5 conda create -y -n tempmoff moff=1.2.1
6 source activate mofftestdata 6 source activate tempmoff
7 7
8 moff_all.py --inputtsv input/mbr_test1.tabular input/mbr_test2.tabular \ 8 moff_all.py --inputtsv input/mbr_test1.tabular input/mbr_test2.tabular \
9 --inputraw input/mbr_test1.mzml input/mbr_test2.mzml \ 9 --inputraw input/mbr_test1.mzml input/mbr_test2.mzml \
10 --tol 10 \ 10 --tol 10 \
11 --rt_w 3 \ 11 --rt_w 3 \
30 --sample mbr_* 30 --sample mbr_*
31 31
32 32
33 # clean up 33 # clean up
34 # mbr outputs for moff all 34 # mbr outputs for moff all
35 rm -r output1/mbr_output 35 rm -r output1/*
36 36
37 # logs 37 rm output2/test_moff_result.txt output2/test__moff.log
38 rm output1/*.log output2/*.log
39 38
40 # peptide summary for all 39 source deactivate tempmoff
41 rm output1/peptide_summary_intensity_moFF_run.tab 40 conda env remove -y -n tempmoff