# HG changeset patch
# User peterjc
# Date 1618612373 0
# Node ID 31a9169b6222d9f8383b86643dca35bbaeac26c7
# Parent  46a667b5e19ea3e3fad848dad74b5c711eeb5ef1
"Update all the pico_galaxy tools on main Tool Shed"

diff -r 46a667b5e19e -r 31a9169b6222 tools/clc_assembly_cell/README.rst
--- a/tools/clc_assembly_cell/README.rst	Wed Feb 01 07:05:09 2017 -0500
+++ b/tools/clc_assembly_cell/README.rst	Fri Apr 16 22:32:53 2021 +0000
@@ -95,6 +95,8 @@
           calling ``clc_cas_to_sam`` in the CLC MApper wrapper.
 v0.0.6  - Update tool XML for optional vs required parameters.
         - Update URLs in documentation.
+v0.0.7  - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
 ======= ======================================================================
 
 
@@ -108,17 +110,17 @@
 Planemo commands (which requires you have set your Tool Shed access details in
 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/
+    $ planemo shed_update -t testtoolshed --check_diff tools/clc_assembly_cell/
     ...
 
 or::
 
-    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/
+    $ planemo shed_update -t toolshed --check_diff tools/clc_assembly_cell/
     ...
 
 To just build and check the tar ball, use::
 
-    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/clc_assembly_cell/
+    $ planemo shed_upload --tar_only tools/clc_assembly_cell/
     ...
     $ tar -tzf shed_upload.tar.gz
     test-data/NC_010642.fna
diff -r 46a667b5e19e -r 31a9169b6222 tools/clc_assembly_cell/clc_assembler.xml
--- a/tools/clc_assembly_cell/clc_assembler.xml	Wed Feb 01 07:05:09 2017 -0500
+++ b/tools/clc_assembly_cell/clc_assembler.xml	Fri Apr 16 22:32:53 2021 +0000
@@ -1,15 +1,10 @@
-<tool id="clc_assembler" name="CLC assembler" version="0.0.6">
+<tool id="clc_assembler" name="CLC assembler" version="0.0.7">
     <description>Assembles reads giving a FASTA file</description>
-    <requirements>
-        <requirement type="binary">clc_assembler</requirement>
-    </requirements>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command>${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command>
-    <command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler
+    <version_command>
+${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version
+    </version_command>
+    <command detect_errors="aggressive">
+\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler
 #for $rg in $read_group
 ##--------------------------------------
 #if str($rg.segments.type) == "paired"
diff -r 46a667b5e19e -r 31a9169b6222 tools/clc_assembly_cell/clc_mapper.xml
--- a/tools/clc_assembly_cell/clc_mapper.xml	Wed Feb 01 07:05:09 2017 -0500
+++ b/tools/clc_assembly_cell/clc_mapper.xml	Fri Apr 16 22:32:53 2021 +0000
@@ -1,46 +1,41 @@
-<tool id="clc_mapper" name="CLC Mapper" version="0.0.6">
+<tool id="clc_mapper" name="CLC Mapper" version="0.0.7">
     <description>Maps reads giving a SAM/BAM file</description>
     <requirements>
-        <requirement type="binary">clc_mapper</requirement>    
-        <requirement type="binary">clc_cas_to_sam</requirement>
-        <requirement type="binary">samtools</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command>${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version</version_command>
-    <command>echo Mapping reads with clc_mapper...
+    <version_command>
+${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version
+    </version_command>
+    <command detect_errors="aggressive">
+echo Mapping reads with clc_mapper...
 &amp;&amp; \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper
 #for $ref in $references
 #if str($ref.ref_type)=="circular"
--d -z "$ref.ref_file"
+-d -z '$ref.ref_file'
 #else
--d "$ref.ref_file"
+-d '$ref.ref_file'
 #end if
 #end for
 #for $rg in $read_group
 ##--------------------------------------
 #if str($rg.segments.type) == "paired"
--p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i "$rg.segments.filename1" "$rg.segments.filename2"
+-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i '$rg.segments.filename1' '$rg.segments.filename2'
 #end if
 ##--------------------------------------
 #if str($rg.segments.type) == "interleaved"
--p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q "$rg.segments.filename"
+-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q '$rg.segments.filename'
 #end if
 ##--------------------------------------
 #if str($rg.segments.type) == "none"
 -p no -q
 #for $f in $rg.segments.filenames
-"$f"
+'$f'
 #end for
 #end if
 ##--------------------------------------
 #end for
 -o "temp_job.cas"
---cpus \${GALAXY_SLOTS:-4}
+--cpus "\${GALAXY_SLOTS:-4}"
 ## TODO - filtering out the progress lines seems to mess up the multiple commands
 ## | grep -v "^Progress: "
 ##===========================================
@@ -48,12 +43,12 @@
 ## use the offset 33, rather then the CLCbio default of 64 which is only for
 ## obsolete Illumina FASTQ files. Really need this option per input file...
 &amp;&amp; echo Converting CAS file to BAM with clc_cas_to_sam...
-&amp;&amp; \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_cas_to_sam --cas "temp_job.cas" -o "temp_job.bam" --no-progress --qualityoffset 33
+&amp;&amp; \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_cas_to_sam --cas 'temp_job.cas' -o 'temp_job.bam' --no-progress --qualityoffset 33
 #if $discard_unmapped:
 ## -u / --discardunmapped: Discard the unmapped reads
 -u
 #end if
-&amp;&amp; rm "temp_job.cas"
+&amp;&amp; rm 'temp_job.cas'
 ##===========================================
 &amp;&amp; echo Sorting BAM file with samtools...
 &amp;&amp; samtools sort "temp_job.bam" "temp_sorted"
@@ -147,7 +142,7 @@
             <param name="read_group_0|segments|dist_mode" value="ss" />
             <param name="read_group_0|segments|filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
             <param name="discard_unmapped" value="false" />
-            <output name="out_fasta" file="SRR639755_mito_pairs_vs_NC_010642_clc.bam" ftype="bam" lines_diff="4"/>
+            <output name="out_bam" file="SRR639755_mito_pairs_vs_NC_010642_clc.bam" ftype="bam" lines_diff="4"/>
         </test>
         <test>
             <param name="ref_file" value="NC_010642.fna" ftype="fasta" />
@@ -160,7 +155,7 @@
             <param name="read_group_0|segments|dist_mode" value="ss" />
             <param name="read_group_0|segments|filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
             <param name="discard_unmapped" value="true" />
-            <output name="out_fasta" file="SRR639755_mito_pairs_vs_NC_010642_clc_u.bam" ftype="bam" lines_diff="4"/>
+            <output name="out_bam" file="SRR639755_mito_pairs_vs_NC_010642_clc_u.bam" ftype="bam" lines_diff="4"/>
         </test>
     </tests>
     <help>
@@ -190,7 +185,7 @@
     <citations>
         <citation type="bibtex">
 @MISC{clcbio,
-AUTHOR = {CLC Bio} 
+AUTHOR = {CLC Bio}
 title = {{CLC Assembly Cell}},
 url = {https://www.qiagenbioinformatics.com/products/clc-assembly-cell/},
 year = {2008--2015}
diff -r 46a667b5e19e -r 31a9169b6222 tools/clc_assembly_cell/tool_dependencies.xml
--- a/tools/clc_assembly_cell/tool_dependencies.xml	Wed Feb 01 07:05:09 2017 -0500
+++ b/tools/clc_assembly_cell/tool_dependencies.xml	Fri Apr 16 22:32:53 2021 +0000
@@ -1,6 +1,6 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="c9bd782f5342"/>
     </package>
-</tool_dependency>
+</tool_dependency>
\ No newline at end of file