Mercurial > repos > galaxyp > proteomics_moff

annotate test-data/make_test_data.sh @ 3:b7512ccf24f6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97
author galaxyp
date Wed, 26 Sep 2018 07:15:19 -0400
parents 5e5c91fab75c
children
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28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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1 #!/bin/bash
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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3 #must be run within tools-galaxyp/tools/moFF/test-data
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41
galaxyp
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5 conda create -y -n tempmoff moff=1.2.1
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41
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6 source activate tempmoff
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28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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8 moff_all.py --inputtsv input/mbr_test1.tabular input/mbr_test2.tabular \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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9 --inputraw input/mbr_test1.mzml input/mbr_test2.mzml \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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10 --tol 10 \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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11 --rt_w 3 \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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12 --rt_p 1 \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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13 --rt_p_match 1.2 \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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14 --peptide_summary 1 \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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15 --output_folder output1
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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17 moff.py --inputtsv input/test.tabular \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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18 --inputraw input/test.mzml \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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19 --tol 10 \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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20 --rt_w 3 \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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21 --rt_p 1 \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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22 --rt_p_match 1.2 \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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23 --peptide_summary 1 \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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24 --output_folder output2
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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25 mv output2/peptide_summary_intensity_moFF_run.tab output2/moff_test_pepsum.tab
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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27 moff_mbr.py \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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28 --inputF input \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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29 --ext tabular \
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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30 --sample mbr_*
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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33 # clean up
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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34 # mbr outputs for moff all
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35 rm -r output1/*
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28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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37 rm output2/test_moff_result.txt output2/test__moff.log
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28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41
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39 source deactivate tempmoff
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41
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40 conda env remove -y -n tempmoff