# HG changeset patch
# User kls286
# Date 1681388291 0
# Node ID a560d5143348efe689f47b7ac7c10dd826de771b
# Parent  3a9135044f146a6a7a3a158be483573695a5da8f
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit e280dd942513f966a9a61a3af68ee7972fb8992f-dirty

diff -r 3a9135044f14 -r a560d5143348 pip_install.sh
--- a/pip_install.sh	Wed Apr 12 19:04:05 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-#!/bin/bash
-
-VERSION=`python --version | awk '{split($2,a,"."); printf "%s.%s", a[1], a[2]}'`
-PIPLOC=`which python | sed 's/bin\/python//g'`
-PIPLOC=$PIPLOC/lib/python$VERSION/site-packages
-echo $PIPLOC
-
-echo 'Try installing $1 to $PIPLOC'
-#pip --exists-action i install --target $PIPLOC $1
-pip install --target $PIPLOC $1
diff -r 3a9135044f14 -r a560d5143348 saxswaxs/ignoreshed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saxswaxs/ignoreshed.yml	Thu Apr 13 12:18:11 2023 +0000
@@ -0,0 +1,7 @@
+name: chap_test_20230328
+owner: kls286
+description: A generic test pipeline for CHAP
+remote_repository_url: https://github.com/CHESSComputing/ChessAnalysisPipeline
+type: unrestricted
+categories:
+- Structural Materials Analysis
diff -r 3a9135044f14 -r a560d5143348 saxswaxs/klspipeline.yaml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saxswaxs/klspipeline.yaml	Thu Apr 13 12:18:11 2023 +0000
@@ -0,0 +1,33 @@
+pipeline:
+
+  # Download example data
+  - common.URLReader:
+      url: https://gitlab01.classe.cornell.edu/api/v4/projects/308/repository/files/saxswaxs%2frawdata_test_1d.tar/raw?ref=main
+      headers:
+        PRIVATE-TOKEN: glpat-sH-sniHbynCxUDJBpv5V # your token here
+  - common.URLResponseProcessor
+  - common.ExtractArchiveWriter:
+      filename: .
+
+  # Collect map data
+  - common.YAMLReader:
+      filename: map.yaml
+      schema: MapConfig
+  - common.MapProcessor
+  - common.NexusWriter:
+      filename: map_specdata.nxs
+      force_overwrite: true
+
+  # Integrate map detetcor data
+  - common.MultipleReader:
+      readers:
+        - YAMLReader:
+            filename: map.yaml
+            schema: MapConfig
+        - YAMLReader:
+            filename: integration.yaml
+            schema: IntegrationConfig
+  - common.IntegrateMapProcessor
+  - common.NexusWriter:
+      filename: map_reduceddata.nxs
+      force_overwrite: true
diff -r 3a9135044f14 -r a560d5143348 saxswaxs/pipeline.yaml
--- a/saxswaxs/pipeline.yaml	Wed Apr 12 19:04:05 2023 +0000
+++ b/saxswaxs/pipeline.yaml	Thu Apr 13 12:18:11 2023 +0000
@@ -4,7 +4,7 @@
   - common.URLReader:
       url: https://gitlab01.classe.cornell.edu/api/v4/projects/308/repository/files/saxswaxs%2frawdata_test_1d.tar/raw?ref=main
       headers:
-        PRIVATE-TOKEN: # your token here
+        PRIVATE-TOKEN: GITLABTOKEN
   - common.URLResponseProcessor
   - common.ExtractArchiveWriter:
       filename: .
diff -r 3a9135044f14 -r a560d5143348 saxswaxs/reduce.xml
--- a/saxswaxs/reduce.xml	Wed Apr 12 19:04:05 2023 +0000
+++ b/saxswaxs/reduce.xml	Thu Apr 13 12:18:11 2023 +0000
@@ -1,6 +1,6 @@
 <tool id="CHAP_saxswaxs_reduce" name="SAXSWAXS Reduce Map" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <requirements>
-      <requirement type="package" version="0.0.3">chessanalysispipeline</requirement>
+      <requirement type="package" version="0.0.5">chessanalysispipeline</requirement>
       <requirement type="package" version="2.28.1">requests</requirement>
       <requirement type="package" version="2023.3.0">pyfai</requirement>
       <requirement type="package" version="1.10.7">pydantic</requirement>
@@ -9,9 +9,11 @@
         pip --exists-action i install certif-pyspec==1.5.3 &&
         cp '$mapconfig' map.yaml &&
 	cp '$integrationconfig' integration.yaml &&
-	CHAP --config '$__tool_directory__/pipeline.yaml'
+	sed 's/GITLABTOKEN/$token/' '$__tool_directory__/pipeline.yaml' > pipeline.yaml
+	CHAP --config pipeline.yaml
     ]]></command>
     <inputs>
+        <param type="text" name="token" />
         <param type="data" name="mapconfig" format="yaml" />
         <param type="data" name="integrationconfig" format="yaml" />
     </inputs>
diff -r 3a9135044f14 -r a560d5143348 tomo/.tmp.tmp.swp
Binary file tomo/.tmp.tmp.swp has changed
diff -r 3a9135044f14 -r a560d5143348 tomo/tmp.tmp
--- a/tomo/tmp.tmp	Wed Apr 12 19:04:05 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-<tool id="CHAP_tomo_reduce" name="Tomo Reduce" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
-    <description>Reduce tomography images</description>
-    <macros>
-        <import>tomo_macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <command detect_errors="exit_code">
-        <![CDATA[
-        $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
-        ls -alh $__tool_directory__/.. &&
-        cp $tool_config reduce.yaml
-        ]]>
-    </command>
-    <configfiles>
-        <configfile name="tool_config">
-            <![CDATA[#slurp
-#*
-#if str($map.type_selector) == "yaml"
-#echo 'detector:' #
-#echo '  file: ' + str($__tool_directory__) + '/andor2.yaml' #
-#end if
-*#
-#echo 'img_x_bounds:' #
-#if str($img_x_bounds.type_selector) == "full_range"
-#echo '- -1' #
-#echo '- -1' #
-#else
-#echo '- ' + str($img_x_bounds.low) #
-#echo '- ' + str($img_x_bounds.upp) #
-#end if
-            ]]>
-        </configfile>
-    </configfiles>
-    <inputs>
-        <conditional name="map">
-            <param name="type_selector" type="select" display="radio" label="Choose map file type">
-                <option value="yaml">YAML</option>
-                <option value="nexus">NeXus</option>
-            </param>
-            <when value="yaml">
-                <param name="input_file" type="data" format="yaml" optional="false" label="Map config file"/>
-                <conditional name="detector">
-                    <param name="type_selector" type="select" display="radio" label="Choose detector prefix">
-                        <option value="andor2">andor2</option>
-                        <option value="manta">manta</option>
-                        <option value="retiga">retiga</option>
-                    </param>
-                    <when value="andor2"/>
-                    <when value="manta"/>
-                    <when value="retiga"/>
-                </conditional>
-            </when>
-            <when value="nexus">
-                <param name="input_file" type="data" format="nex" optional="false" label="Tomography setup file"/>
-            </when>
-        </conditional>
-        <conditional name="img_x_bounds">
-            <param name="type_selector" type="select" label="Choose vertical detector image bounds">
-                <option value="full_range" selected="true">Use the full image range</option>
-                <option value="enter_range">Manually enter the image range</option>
-            </param>
-            <when value="full_range"/>
-            <when value="enter_range">
-                <param name="low" type="integer" value="-1" optional="false" label="Lower image range index"/>
-                <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reduce.yaml" hidden="false"/>
-    </outputs>
-    <help>
-        <![CDATA[
-        usage: PROG [-h] [--config CONFIG] [--verbose]
-
-options:
-  -h, --help       show this help message and exit
-  --config CONFIG  Input configuration file
-  --verbose        verbose output
-
-        ]]>
-    </help>
-    <expand macro="citations"/>
-</tool>
diff -r 3a9135044f14 -r a560d5143348 tomo/tomo_macros.xml
--- a/tomo/tomo_macros.xml	Wed Apr 12 19:04:05 2023 +0000
+++ b/tomo/tomo_macros.xml	Thu Apr 13 12:18:11 2023 +0000
@@ -1,10 +1,10 @@
 <macros>
     <token name="@TOOL_VERSION@">0.1.0</token>
     <token name="@PROFILE@">21.09</token>
-    <token name="@PYTHON_TEMPLATE_VERSION@">3.9</token>
+    <token name="@PYTHON_TEMPLATE_VERSION@">3.9.13</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.0.4">chessanalysispipeline</requirement>
+            <requirement type="package" version="0.0.3">chessanalysispipeline</requirement>
             <requirement type="package" version="1.1.0">lmfit</requirement>
             <requirement type="package" version="3.7.1">matplotlib</requirement>
             <requirement type="package" version="1.0.1">nexusformat</requirement>
diff -r 3a9135044f14 -r a560d5143348 tomo/tomo_reduce.xml
--- a/tomo/tomo_reduce.xml	Wed Apr 12 19:04:05 2023 +0000
+++ b/tomo/tomo_reduce.xml	Thu Apr 13 12:18:11 2023 +0000
@@ -7,33 +7,32 @@
     <command detect_errors="exit_code">
         <![CDATA[
         mkdir tomo_reduce_plots;
-        $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
-        #if str($map.type_selector) == "yaml"
-            cp $input_file map.yaml &&
-            cat $__tool_directory__/andor2.yaml $tool_config > reduce.yaml &&
+        pip --exists-action i install certif-pyspec==1.5.3 &&
+        #if str($map.type_selector) == "YAML"
+            cp '$input_file' map.yaml &&
         #else
-            cp $input_file setup.nex &&
-            cp $tool_config reduce.yaml &&
+            cp '$input_file' setup.nex &&
         #end if
+        cp '$tool_config' reduce.yaml &&
         CHAP --config 
-        #if str($map.type_selector) == "yaml"
-            $__tool_directory__/pipeline_reduce_yaml.yaml
+        #if str($map.type_selector) == "YAML"
+            '$__tool_directory__/pipeline_reduce_yaml.yaml'
         #else
-            $__tool_directory__/pipeline_reduce_nexus.yaml
+            '$__tool_directory__/pipeline_reduce_nexus.yaml'
         #end if
         ]]>
     </command>
     <configfiles>
         <configfile name="tool_config">
             <![CDATA[#slurp
-#echo 'img_x_bounds:' #
-#if str($img_x_bounds.type_selector) == "full_range"
-#echo '- -1' #
-#echo '- -1' #
-#else
-#echo '- ' + str($img_x_bounds.low) #
-#echo '- ' + str($img_x_bounds.upp) #
-#end if
+                #echo 'img_x_bounds:' #
+                #if str($img_x_bounds.type_selector) == "full_range"
+                    #echo '- -1'
+                    #echo '- -1'
+                #else
+                    #echo '- ' + str($img_x_bounds.low)
+                    #echo '- ' + str($img_x_bounds.upp)
+                #end if
             ]]>
         </configfile>
     </configfiles>