diff 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/make_test_data.sh	Fri Jan 05 12:47:36 2018 -0500
@@ -0,0 +1,41 @@
+#!/bin/bash
+
+#must be run within tools-galaxyp/tools/moFF/test-data
+
+conda create -n mofftestdata moff
+source activate mofftestdata
+
+moff_all.py --inputtsv input/mbr_test1.tabular input/mbr_test2.tabular \
+    --inputraw input/mbr_test1.mzml input/mbr_test2.mzml \
+    --tol 10 \
+    --rt_w 3 \
+    --rt_p 1 \
+    --rt_p_match 1.2 \
+    --peptide_summary 1 \
+    --output_folder output1
+
+moff.py --inputtsv input/test.tabular \
+    --inputraw input/test.mzml \
+    --tol 10 \
+    --rt_w 3 \
+    --rt_p 1 \
+    --rt_p_match 1.2 \
+    --peptide_summary 1 \
+    --output_folder output2
+mv output2/peptide_summary_intensity_moFF_run.tab output2/moff_test_pepsum.tab
+
+moff_mbr.py \
+    --inputF input \
+    --ext tabular \
+    --sample mbr_*
+
+
+# clean up 
+# mbr outputs for moff all
+rm -r output1/mbr_output
+
+# logs
+rm output1/*.log output2/*.log
+
+# peptide summary for all
+rm output1/peptide_summary_intensity_moFF_run.tab