Mercurial > repos > mbernt > maxbin2
comparison maxbin2.xml @ 3:cfd50144a871 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit fe30b00aa09587876f4c8be2a1494ca5ef6b8bac"
author | iuc |
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date | Sun, 01 Dec 2019 09:42:33 -0500 |
parents | 6a638de7915c |
children | 4ef88f9a195d |
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2:6a638de7915c | 3:cfd50144a871 |
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1 <tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy1"> | 1 <tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy2"> |
2 <description>clusters metagenomic contigs into bins</description> | 2 <description>clusters metagenomic contigs into bins</description> |
3 <macros> | 3 <macros> |
4 <token name="@MAXBIN_VERSION@">2.2.7</token> | 4 <token name="@MAXBIN_VERSION@">2.2.7</token> |
5 </macros> | 5 </macros> |
6 <requirements> | 6 <requirements> |
47 $adv_cond.plotmarker | 47 $adv_cond.plotmarker |
48 -markerset $adv_cond.markerset | 48 -markerset $adv_cond.markerset |
49 #end if | 49 #end if |
50 -thread \${GALAXY_SLOTS:-1} | 50 -thread \${GALAXY_SLOTS:-1} |
51 | 51 |
52 && tar -xf out.marker_of_each_bin.tar.gz | 52 && gzip -cd out.marker_of_each_bin.tar.gz | tar -xf - |
53 | 53 |
54 ## redirect the idba out and err file content to stdout and err | 54 ## redirect the idba out and err file content to stdout and err |
55 ## since this is also wanted in case the error case ';' is used here to | 55 ## since this is also wanted in case the error case ';' is used here to |
56 ## separate commands | 56 ## separate commands |
57 #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != "" | 57 #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != "" |
58 ; echo "==== IDBA stdout ====" | 58 ; echo "==== IDBA stdout ====" |
59 && cat out.idba.out | 59 && if [[ -f out.idba.out ]]; then cat out.idba.out; fi |
60 && echo "==== IDBA stderr ====" 1>&2 | 60 && echo "==== IDBA stderr ====" 1>&2 |
61 && cat out.idba.err 1>&2 | 61 && if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi |
62 #end if | 62 #end if |
63 ]]></command> | 63 ]]></command> |
64 <inputs> | 64 <inputs> |
65 <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/> | 65 <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/> |
66 <conditional name="intype_cond"> | 66 <conditional name="intype_cond"> |
140 <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string} (reassembly N50)" from_work_dir="out.reassem/N50.txt"> | 140 <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string} (reassembly N50)" from_work_dir="out.reassem/N50.txt"> |
141 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter> | 141 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter> |
142 </data> | 142 </data> |
143 </outputs> | 143 </outputs> |
144 <tests> | 144 <tests> |
145 <test expect_num_outputs="4"><!-- test w contigs and reads as input --> | 145 <!-- test w contigs and reads as input --> |
146 <test expect_num_outputs="4"> | |
146 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" /> | 147 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" /> |
147 <conditional name="intype_cond"> | 148 <conditional name="intype_cond"> |
148 <param name="intype_select" value="rds"/> | 149 <param name="intype_select" value="rds"/> |
149 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/> | 150 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/> |
150 </conditional> | 151 </conditional> |