Mercurial > repos > iuc > kc_align

comparison kc-align.xml @ 11:c7d4789dd859 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit de05aab169e4fc4ee7130411d0081741bb246ce2
author iuc
date Fri, 24 Jun 2022 15:56:58 +0000
parents 341c8de8b5fb
children
comparison
equal deleted inserted replaced
10:341c8de8b5fb 11:c7d4789dd859
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>
2 <xrefs> 6 <xrefs>
3 <xref type="bio.tools">kallisto</xref> 7 <xref type="bio.tools">kc-align</xref>
4 </xrefs> 8 </xrefs>
5 <requirements> 9 <requirements>
6 <requirement type="package" version="1.0.2">kcalign</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">kcalign</requirement>
7 </requirements> 11 </requirements>
8 <command detect_errors="exit_code"> 12 <command detect_errors="exit_code">
9 <![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
10 kc-align 25 kc-align
11 --mode '$position.mode' 26 --mode '$position.mode'
12 --reference '$ref' 27 --reference '$ref'
13 --sequences '$seqs' 28 --sequences '$seqs'
14 #if $position.mode == "genome": 29 #if $position.mode == "genome":
18 #end if 33 #end if
19 #if $position.mode == "mixed": 34 #if $position.mode == "mixed":
20 -d '$position.dist' 35 -d '$position.dist'
21 #end if 36 #end if
22 $compress 37 $compress
23 -th \${GALAXY_SLOTS:-1} 38 -th "\$SLOTS"
24 39
25 ]]></command> 40 ]]></command>
26 <inputs> 41 <inputs>
27 <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" />
28 <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" />