clc_assembly_cell: tools/clc_assembly_cell/clc

comparison tools/clc_assembly_cell/clc_mapper.xml @ 5:31a9169b6222 draft default tip

"Update all the pico_galaxy tools on main Tool Shed"

author	peterjc
date	Fri, 16 Apr 2021 22:32:53 +0000
parents	46a667b5e19e
children

comparison

equal deleted inserted replaced

-:46a667b5e19e
+:31a9169b6222
-<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>
+<version_command>
-<!-- Assume anything other than zero is an error -->
+${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version
-<exit_code range="1:" />
+</version_command>
-<exit_code range=":-1" />
+<command detect_errors="aggressive">
-</stdio>
+echo Mapping reads with clc_mapper...
-<version_command>${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version</version_command>
-<command>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: "
 ##===========================================
 ## TODO - I've required all the input in Sanger FASTQ format (or FASTA) so can
 ## 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 $discard_unmapped:
 ## -u / --discardunmapped: Discard the unmapped reads
 -u
 #end if
-&amp;&amp; rm "temp_job.cas"
+&amp;&amp; rm 'temp_job.cas'
 ##===========================================
 &amp;&amp; echo Sorting BAM file with samtools...
 &amp;&amp; samtools sort "temp_job.bam" "temp_sorted"
 &amp;&amp; mv "temp_sorted.bam" "$out_bam"
 &amp;&amp; echo Indexing BAM file with samtools...
 <param name="read_group_0|segments|min_size" value="1" />
 <param name="read_group_0|segments|max_size" value="1000" />
 <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" />
 <param name="ref_type" value="circular" />
 <param name="read_group_0|segments|type" value="interleaved" />
 <param name="read_group_0|segments|min_size" value="1" />
 <param name="read_group_0|segments|max_size" value="1000" />
 <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>
 **What it does**
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
 </help>
 <citations>
 <citation type="bibtex">
 @MISC{clcbio,
 AUTHOR = {CLC Bio}
 title = {{CLC Assembly Cell}},
 url = {https://www.qiagenbioinformatics.com/products/clc-assembly-cell/},
 year = {2008--2015}
 }
 </citation>

Mercurial > repos > peterjc > clc_assembly_cell

comparison tools/clc_assembly_cell/clc_mapper.xml @ 5:31a9169b6222 draft default tip