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comparison kc-align.xml @ 10:97476dfde728 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit de05aab169e4fc4ee7130411d0081741bb246ce2
author iuc
date Fri, 24 Jun 2022 15:57:35 +0000
parents 0c0288a9d92c
children
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9:0c0288a9d92c 10:97476dfde728
1 <tool id="kc-align" name="Kc-Align" version="1.0.2" python_template_version="3.5"> 1 <tool id="kc-align" name="Kc-Align" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <macros>
3 <token name="@TOOL_VERSION@">1.0.2</token>
4 <token name="@VERSION_SUFFIX@">1</token>
5 </macros>
6 <xrefs>
7 <xref type="bio.tools">kc-align</xref>
8 </xrefs>
2 <requirements> 9 <requirements>
3 <requirement type="package" version="1.0.2">kcalign</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">kcalign</requirement>
4 </requirements> 11 </requirements>
5 <command detect_errors="exit_code"> 12 <command detect_errors="exit_code">
6 <![CDATA[ 13 <![CDATA[
14 ## number of slots needs to be one or divisible by three
15 SLOTS=\${GALAXY_SLOTS:-1};
16 while [ \$SLOTS -gt 1 ];
17 do
18 if ! (( \$SLOTS % 3 )) ; then break; fi;
19 ((SLOTS--));
20 done;
21 if [[ "\${GALAXY_SLOTS:-1}" -ne "\$SLOTS" ]]; then
22 >&2 echo "Warning: using only \$SLOTS threads (instead of the configured \${GALAXY_SLOTS:-1}), since it needs to be 1 or a multiple of three. Please contact your Galaxy Admin";
23 fi;
24
7 kc-align 25 kc-align
8 --mode '$position.mode' 26 --mode '$position.mode'
9 --reference '$ref' 27 --reference '$ref'
10 --sequences '$seqs' 28 --sequences '$seqs'
11 #if $position.mode == "genome": 29 #if $position.mode == "genome":
15 #end if 33 #end if
16 #if $position.mode == "mixed": 34 #if $position.mode == "mixed":
17 -d '$position.dist' 35 -d '$position.dist'
18 #end if 36 #end if
19 $compress 37 $compress
20 -th \${GALAXY_SLOTS:-1} 38 -th "\$SLOTS"
21 39
22 ]]></command> 40 ]]></command>
23 <inputs> 41 <inputs>
24 <param name="ref" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" /> 42 <param name="ref" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" />
25 <param name="seqs" type="data" format="fasta" label="Reads" help="Multi-FASTA of seqeunces to be aligned with the reference" /> 43 <param name="seqs" type="data" format="fasta" label="Reads" help="Multi-FASTA of seqeunces to be aligned with the reference" />