From 2fc72737a83bb2cf50e7883f6907fb229f8c9f12 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Wed, 27 May 2015 20:41:13 +0200
Subject: [PATCH] properly implemented the input for define_output
Takes now the fusion - deconvolution switch into account.
---
spim_registration/timelapse/Snakefile | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 36d8cfb..00ba40f 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -19,6 +19,7 @@ rule done:
#input: [ ds + "_" + config["common"]["fusion_switch"] for ds in datasets ]
#input: config["hdf5_output"]["output_xml"] + ".xml"
input: [ ds + "_output_hdf5" for ds in datasets ]
+ #input: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
rule resave_prepared:
input: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"] ], suffix=["xml","h5"])
@@ -376,7 +377,7 @@ rule deconvolution:
shell(cmd_string)
rule define_output:
- input: glob.glob('TP*')
+ input: [ item + "_" + config["common"]["fusion_switch"] for item in datasets ], glob.glob('TP*')
output: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
log: "define_xml_tif.log"
run:
@@ -409,8 +410,8 @@ rule define_output:
# create mother .xml/.h5
rule hdf5_xml_output:
input: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
- output: expand("{dataset}.{suffix}",dataset=[ config["hdf5_output"]["output_hdf5_xml"].strip('\"')], suffix=["xml","h5"]),
- [ item+"_output" for item in datasets ]
+ output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]),
+ [ item+"_output" for item in datasets ] # expand("{dataset}.{suffix}",dataset=[ config["hdf5_output"]["output_hdf5_xml"].strip('\"')], suffix=["xml","h5"]), "{xml_base}-{file_id,\d+}-00.h5_output_hdf5_xml"
log: "hdf5_xml.log"
run:
part_string = produce_string(
--
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