Mercurial > repos > iuc > samtools_fastx

annotate samtools_fastx.xml @ 2:af994f4458bc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:31:10 -0400
parents a5429e2e18e8
children c933a9166b1d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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1 <tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy1">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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2 <description>extract FASTA or FASTQ from alignment files</description>
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
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3 <macros>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
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4 <import>macros.xml</import>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
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5 </macros>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
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6 <expand macro="requirements" />
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a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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7 <expand macro="stdio"/>
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
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8 <expand macro="version_command" />
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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9 <command><![CDATA[
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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10 @ADDTHREADS@
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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11 ## name sort input file if neccessary
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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12 #if not $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'):
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af994f4458bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
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13 samtools sort -@ \$addthreads -n '$input' -T "\${TMPDIR:-.}" > input &&
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a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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14 #else:
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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15 ln -s '$input' input &&
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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16 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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17
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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18 #set command=str($output_fmt_cond.output_fmt_select)[:5]
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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19
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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20 samtools $command
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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21 #if str($output_fmt_cond.output_fmt_select).startswith('fastq'):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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22 #if str($output_fmt_cond.default_quality) != '':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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23 -v $output_fmt_cond.default_quality
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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24 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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25 $output_fmt_cond.output_quality
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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26 $output_fmt_cond.ilumina_casava
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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27 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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28 $copy_tags
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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29 #if str($copy_arb_tags) != '':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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30 -T '$copy_arb_tags'
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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31 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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32 $read_numbering
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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33 #if 'r0' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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34 -0 nonspecific.$output_fmt_cond.output_fmt_select
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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35 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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36 #if 'r1' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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37 -1 forward.$output_fmt_cond.output_fmt_select
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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38 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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39 #if 'r2' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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40 -2 reverse.$output_fmt_cond.output_fmt_select
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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41 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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42 #if str($inclusive_filter) != 'None':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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43 #set $filter = $inclusive_filter
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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44 @FLAGS@
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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45 -f $flags
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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46 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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47 #if str($exclusive_filter) != 'None':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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48 #set $filter = $exclusive_filter
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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49 @FLAGS@
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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50 -F $flags
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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51 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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52 #if str($exclusive_filter) != 'None':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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53 #set $filter = $exclusive_filter_all
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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54 @FLAGS@
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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55 -G $flags
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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56 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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57 #if 's' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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58 -s singletons.$output_fmt_cond.output_fmt_select
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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59 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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60 #if str($idxout_cond.idxout_select) == 'yes':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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61 #if str($idxout_cond.write1st) == 'yes':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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62 --i1 i1.$output_fmt_cond.output_fmt_select
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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63 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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64 #if str($idxout_cond.write2nd) == 'yes':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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65 --i2 i2.$output_fmt_cond.output_fmt_select
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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66 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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67 #if str($idxout_cond.index_format) != '':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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68 --index-format $idxout_cond.index_format
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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69 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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70 #if str($idxout_cond.barcode_tag) != '':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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71 --barcode-tag $idxout_cond.barcode_tag
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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72 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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73 #if str($idxout_cond.quality_tag) != '':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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74 --quality-tag $idxout_cond.quality_tag
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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75 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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76 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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77
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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78 input
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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79
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80 #if str($outputs)=='None' or 'other' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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81 ## since currently stdout in not zipped (samtools doesn't know about the extension)
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82 #if str($output_fmt_cond.output_fmt_select).endswith('.gz'):
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83 | gzip -
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84 #end if
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85 > output.$output_fmt_cond.output_fmt_select
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86 && ln -s output.$output_fmt_cond.output_fmt_select output
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87 #else
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88 ## otherwise the remaining sequences would show up in the datasets info box
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89 > /dev/null
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90 #end if
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91 #if 'r0' in str($outputs):
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92 && ln -s nonspecific.$output_fmt_cond.output_fmt_select nonspecific
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93 #end if
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94 #if 'r1' in str($outputs):
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95 && ln -s forward.$output_fmt_cond.output_fmt_select forward
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96 #end if
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97 #if 'r2' in str($outputs):
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98 && ln -s reverse.$output_fmt_cond.output_fmt_select reverse
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99 #end if
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100 #if 's' in str($outputs):
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101 && ln -s singletons.$output_fmt_cond.output_fmt_select singletons
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102 #end if
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103 #if str($idxout_cond.idxout_select) == 'yes':
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104 #if str($idxout_cond.write1st) == 'yes':
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105 && ln -s i1.$output_fmt_cond.output_fmt_select i1
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106 #end if
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107 #if str($idxout_cond.write2nd) == 'yes':
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108 && ln -s i2.$output_fmt_cond.output_fmt_select i2
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109 #end if
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110 #end if
0
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111 ]]>
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112 </command>
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113 <inputs>
1
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114 <param name="input" type="data" format="sam,bam,cram" label="BAM or SAM file to convert" />
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115 <conditional name="output_fmt_cond">
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116 <param name="output_fmt_select" type="select" label="Output format">
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117 <option value="fasta" selected="True">FASTA</option>
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118 <option value="fastqsanger">FASTQ</option>
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119 <option value="fasta.gz">compressed FASTA</option>
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120 <option value="fastqsanger.gz">compressed FASTQ</option>
0
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121 </param>
1
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122 <when value="fastqsanger">
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123 <param name="default_quality" argument="-v" type="integer" optional="True" label="Default quality if none is given" />
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124 <param name="output_quality" argument="-O" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Output quality in the OQ tag if available" />
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125 <param name="ilumina_casava" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)" />
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
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126 </when>
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127 <when value="fasta" />
1
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128 <when value="fastqsanger.gz">
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129 <param name="default_quality" argument="-v" type="integer" optional="True" label="Default quality if none is given" />
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130 <param name="output_quality" argument="-O" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Output quality in the OQ tag if available" />
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131 <param name="ilumina_casava" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)" />
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132 </when>
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133 <when value="fasta.gz" />
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134 </conditional>
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135 <param name="outputs" type="select" multiple="true" label="outputs">
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136 <option value="other" selected="true">others</option>
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137 <option value="r1">READ1</option>
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138 <option value="r2">READ2</option>
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139 <option value="s">singletons</option>
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140 <option value="r0">unspecific</option>
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141 <help>disjoint subsets of the reads can be redirected to separate data sets. "READ[12]" are reads for which the READ[12] flag is set and the READ[21] flag is not set. "unspecific" reads are those for which both ore neither of these flags are set. "singletons" are the singleto reads. Note that if selected READ1 and READ2 contain only the paired reads. "other" are the remaining reads. If onlz 'others' or nothing is selected all reads go to a single data set. </help>
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142 </param>
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143 <param name="copy_tags" argument="-t" type="boolean" truevalue="-t" falsevalue="" label="Copy RG/BC/QT tags to output header" />
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144 <param name="copy_arb_tags" argument="-T" type="text" optional="true" label="copy arbitrary tags to the FASTA header line" />
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145 <param name="read_numbering" type="select" label="Omit or append read numbers">
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146 <option value="" selected="True">no</option>
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147 <option value="-n">Do not append /1 and /2 to read names</option>
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148 <option value="-N">always append /1 and /2 to read name</option>
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149 </param>
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150 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
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151 <expand macro="flag_options" />
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152 </param>
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153 <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
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154 <expand macro="flag_options" />
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155 </param>
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156 <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set">
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157 <expand macro="flag_options" />
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158 </param>
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159
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160 <conditional name="idxout_cond">
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161 <param name="idxout_select" type="select" label="Write index read files">
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162 <option value="no" selected="True">No</option>
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163 <option value="yes">Yes (beta: feedback welcome)</option>
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164 </param>
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165 <when value="no" />
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166 <when value="yes">
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167 <param name="write1st" argument="--i1" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="write first index reads to extra data set" />
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168 <param name="write2nd" argument="--i2" type="boolean" truevalue="yes" falsevalue="no" checked='true' label="write second index reads to extra data set" />
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169 <param name="index_format" argument="--index-format" type="text" label="Index format: How to parse barcode and quality tags">
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170 <help>
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171 The index-format string describes how to parse the barcode and quality tags, for example:
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172 i14i8 the first 14 characters are index 1, the next 8 characters are index 2
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173 n8i14 ignore the first 8 characters, and use the next 14 characters for index 1
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174 If the tag contains a separator, then the numeric part can be replaced with '*' to mean
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175 'read until the separator or end of tag', for example:
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176 n*i* ignore the left part of the tag until the separator, then use the second part
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177 of the tag as index 1
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178 </help>
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179 </param>
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180 <param name="barcode_tag" argument="--barcode-tag" type="text" optional="True" label="Barcode tag [default: BC]"/>
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181 <param name="quality_tag" argument="--quality-tag" type="text" optional="True" label="Quality tag [default: QT]"/>
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182 </when>
0
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183 </conditional>
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184 </inputs>
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185 <outputs>
1
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186 <data name="nonspecific" format="fasta" from_work_dir="nonspecific" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (nonspecific)">
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187 <filter>'r0' in str(outputs)</filter>
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188 <actions>
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189 <action type="format">
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190 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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191 </action>
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192 </actions>
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193 </data>
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194 <data name="forward" format="fasta" from_work_dir="forward" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (READ1)">
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195 <filter>'r1' in str(outputs)</filter>
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196 <actions>
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197 <action type="format">
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198 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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199 </action>
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200 </actions>
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201 </data>
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202 <data name="reverse" format="fasta" from_work_dir="reverse" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (READ2)">
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203 <filter>'r2' in str(outputs)</filter>
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204 <actions>
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205 <action type="format">
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206 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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207 </action>
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208 </actions>
0
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209 </data>
1
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210 <data name="singletons" format="fasta" from_work_dir="singletons" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (singletons)">
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211 <filter>'s' in str(outputs)</filter>
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212 <actions>
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213 <action type="format">
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214 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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215 </action>
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216 </actions>
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217 </data>
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218 <data name="output" format="fasta" from_work_dir="output" label="${on_string} converted to ${output_fmt_cond.output_fmt_select}">
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219 <filter>str(outputs)=='None' or 'other' in str(outputs)</filter>
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220 <actions>
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221 <action type="format">
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222 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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223 </action>
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224 </actions>
0
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225 </data>
1
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226 <data name="i1" format="fasta" from_work_dir="i1" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (1st index)">
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227 <filter>idxout_cond['idxout_select']=='yes' and idxout_cond['write1st']</filter>
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228 <actions>
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229 <action type="format">
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230 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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231 </action>
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232 </actions>
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233 </data>
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234 <data name="i2" format="fasta" from_work_dir="i2" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (2nd index)">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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235 <filter>idxout_cond['idxout_select']=='yes' and idxout_cond['write2nd']</filter>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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236 <actions>
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237 <action type="format">
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238 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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239 </action>
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240 </actions>
0
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241 </data>
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242 </outputs>
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243 <tests>
1
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244 <!-- tests from original Galaxy tool -->
0
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245 <test>
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246 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
1
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247 <conditional name="output_fmt_cond">
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248 <param name="output_fmt_select" value="fasta" />
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249 </conditional>
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250 <param name="outputs" value="other" />
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251 <output name="output" file="samtools_fastx-out1.fasta" ftype="fasta" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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252 </test>
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253 <test>
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254 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
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255 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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256 <param name="output_fmt_select" value="fastqsanger" />
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257 </conditional>
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258 <param name="outputs" value="r0,r1,r2" />
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259 <output name="nonspecific" file="samtools_fastx-out2-1.fastq" ftype="fastqsanger" />
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260 <output name="forward" file="samtools_fastx-out2-2.fastq" ftype="fastqsanger" />
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261 <output name="reverse" file="samtools_fastx-out2-3.fastq" ftype="fastqsanger" />
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262 </test>
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263 <test>
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264 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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265 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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266 <param name="output_fmt_select" value="fasta" />
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267 </conditional>
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268 <param name="outputs" value="r0,r1,r2" />
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269 <output name="nonspecific" file="samtools_fastx-out3-1.fasta" ftype="fasta" />
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270 <output name="forward" file="samtools_fastx-out3-2.fasta" ftype="fasta" />
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271 <output name="reverse" file="samtools_fastx-out3-3.fasta" ftype="fasta" />
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272 </test>
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273 <!-- tests from original Galaxy tool with gz output. for some reason gzip (which is used
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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274 for compressing stdout does not give exactly the same file contents .. the other
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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275 compressed files seem to)-->
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276 <test>
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277 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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278 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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279 <param name="output_fmt_select" value="fasta.gz" />
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280 </conditional>
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281 <param name="outputs" value="other" />
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282 <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" compare="sim_size" />
0
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283 </test>
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284 <test>
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285 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
1
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286 <conditional name="output_fmt_cond">
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287 <param name="output_fmt_select" value="fastqsanger.gz" />
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288 </conditional>
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289 <param name="outputs" value="r0,r1,r2" />
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290 <output name="nonspecific" file="samtools_fastx-out2-1.fastq.gz" ftype="fastqsanger.gz" />
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291 <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" />
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292 <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" />
0
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293 </test>
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294 <test>
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295 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
1
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296 <conditional name="output_fmt_cond">
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297 <param name="output_fmt_select" value="fasta.gz" />
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298 </conditional>
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299 <param name="outputs" value="r0,r1,r2" />
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300 <output name="nonspecific" file="samtools_fastx-out3-1.fasta.gz" ftype="fasta.gz" />
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301 <output name="forward" file="samtools_fastx-out3-2.fasta.gz" ftype="fasta.gz" />
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302 <output name="reverse" file="samtools_fastx-out3-3.fasta.gz" ftype="fasta.gz" />
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303 </test>
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304 <!-- tests from: https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2313-->
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305 <!--# basic 2 output test without singleton tracking-->
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306 <!--test_cmd($opts, out=>'bam2fq/1.stdout.expected', out_map=>{'1.fq' => 'bam2fq/1.1.fq.expected', '2.fq' => 'bam2fq/1.2.fq.expected'},cmd=>"$$opts{bin}/samtools fastq @$threads -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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307 <test>
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308 <param name="input" value="bam2fq.001.sam" ftype="sam" />
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309 <conditional name="output_fmt_cond">
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310 <param name="output_fmt_select" value="fastqsanger" />
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311 </conditional>
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312 <param name="outputs" value="r1,r2,other" />
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313 <output name="forward" file="1.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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314 <output name="reverse" file="1.2.fq.expected" ftype="fastqsanger" />
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315 <output name="output" file="1.stdout.expected" ftype="fastqsanger" />
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316 </test>
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317 <!--# basic 2 output test with singleton tracking but no singleton-->
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318 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/2.1.fq.expected', '2.fq' => 'bam2fq/2.2.fq.expected', 's.fq' => 'bam2fq/2.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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319 <test>
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320 <param name="input" value="bam2fq.001.sam" ftype="sam" />
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321 <conditional name="output_fmt_cond">
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322 <param name="output_fmt_select" value="fastqsanger" />
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323 </conditional>
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324 <param name="outputs" value="r1,r2,s,other" />
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325 <output name="forward" file="2.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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326 <output name="reverse" file="2.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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327 <output name="singletons" file="2.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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328 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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329 </test>
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330 <!--# basic 2 output test with singleton tracking with a singleton in the middle-->
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331 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/3.1.fq.expected', '2.fq' => 'bam2fq/3.2.fq.expected', 's.fq' => 'bam2fq/3.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.002.sam");-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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332 <test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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333 <param name="input" value="bam2fq.002.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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334 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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335 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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336 </conditional>
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337 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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338 <output name="forward" file="3.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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339 <output name="reverse" file="3.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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340 <output name="singletons" file="3.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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341 <output name="output" file="3.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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342 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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343 <!--# basic 2 output test with singleton tracking with a singleton as last read-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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344 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.003.sam");-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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345 <test>
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346 <param name="input" value="bam2fq.003.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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347 <conditional name="output_fmt_cond">
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348 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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349 </conditional>
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350 <param name="outputs" value="r1,r2,s,other" />
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351 <output name="forward" file="4.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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352 <output name="reverse" file="4.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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353 <output name="singletons" file="4.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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354 <output name="output" file="4.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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355 </test>
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356 <!--# tag output test with singleton tracking with a singleton as last read-->
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357 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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358 <test>
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359 <param name="input" value="bam2fq.004.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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360 <conditional name="output_fmt_cond">
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361 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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362 </conditional>
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363 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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364 <conditional name="idxout_cond">
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365 <param name="idxout_select" value="yes"/>
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366 <param name="write1st" value="yes"/>
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367 <param name="barcode_tag" value="BC"/>
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368 <param name="index_format" value="n2i2"/>
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369 </conditional>
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370 <output name="forward" file="4.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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371 <output name="reverse" file="4.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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372 <output name="singletons" file="4.s.fq.expected" ftype="fastqsanger" />
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373 <output name="output" file="4.stdout.expected" ftype="fastqsanger" />
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374 <output name="i1" file="bc.fq.expected" ftype="fastqsanger" />
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375 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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376 <!--# test -O flag with no OQ tags-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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377 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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378 <test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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379 <param name="input" value="bam2fq.010.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
380 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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381 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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382 <param name="output_quality" value="-O" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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383 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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parents: 0
diff changeset
384 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
385 <conditional name="idxout_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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386 <param name="idxout_select" value="yes"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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387 <param name="write1st" value="yes"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
388 <param name="barcode_tag" value="BC"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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389 <param name="index_format" value="n2i2"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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390 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
391 <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
392 <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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393 <output name="singletons" file="10.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
394 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
395 <output name="i1" file="bc10.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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396 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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397 <!--# test -O flag with OQ tags-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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398 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/10.1.fq.expected', '2.fq' => 'bam2fq/10.2.fq.expected', 's.fq' => 'bam2fq/10.s.fq.expected', 'bc.fq' => 'bam2fq/bc10.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.010.sam");-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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399 <test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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400 <param name="input" value="bam2fq.010.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
401 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
402 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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403 <param name="output_quality" value="-O" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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404 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
405 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
406 <conditional name="idxout_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
407 <param name="idxout_select" value="yes"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
408 <param name="write1st" value="yes"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
409 <param name="barcode_tag" value="BC"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
410 <param name="index_format" value="n2i2"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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411 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
412 <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
413 <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
414 <output name="singletons" file="10.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
415 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
416 <output name="i1" file="bc10.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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417 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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418 <!--# tag output test with separators and -N flag-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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419 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/5.1.fq.expected', '2.fq' => 'bam2fq/5.2.fq.expected', 's.fq' => 'bam2fq/5.s.fq.expected', 'bc_split.fq' => 'bam2fq/bc_split.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -N \-\-index-format 'n*i*' \-\-i1 $$opts{path}/bc_split.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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420 <test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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421 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
422 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
423 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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424 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
425 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
426 <param name="read_numbering" value="-N"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
427 <conditional name="idxout_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
428 <param name="idxout_select" value="yes"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
429 <param name="write1st" value="yes"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
430 <param name="barcode_tag" value="BC"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
431 <param name="index_format" value="n*i*"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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432 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
433 <output name="forward" file="5.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
434 <output name="reverse" file="5.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
435 <output name="singletons" file="5.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
436 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
437 <output name="i1" file="bc_split.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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438 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
439 <!--# -t flag-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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440 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/6.1.fq.expected', '2.fq' => 'bam2fq/6.2.fq.expected', 's.fq' => 'bam2fq/6.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
441 <test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
442 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
443 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
444 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
445 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
446 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
447 <param name="copy_tags" value="-t" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
448 <param name="read_numbering" value="-N"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
449 <output name="forward" file="6.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
450 <output name="reverse" file="6.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
451 <output name="singletons" file="6.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
452 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
453 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
454 <!--# -T flag-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
455 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
456 <test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
457 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
458 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
459 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
460 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
461 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
462 <param name="copy_tags" value="-t" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
463 <param name="copy_arb_tags" value="MD,ia" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
464 <param name="read_numbering" value="-N"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
465 <output name="forward" file="7.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
466 <output name="reverse" file="7.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
467 <output name="singletons" file="7.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
468 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
469 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
470 <!--# -i flag with no index-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
471 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -i -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
472 <test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
473 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
474 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
475 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
476 <param name="ilumina_casava" value="-i" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
477 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
478 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
479 <param name="copy_tags" value="-t" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
480 <param name="copy_arb_tags" value="MD,ia" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
481 <param name="read_numbering" value="-N"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
482 <output name="forward" file="7.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
483 <output name="reverse" file="7.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
484 <output name="singletons" file="7.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
485 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
486 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
487 <!--# -i flag with index-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
488 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/8.1.fq.expected', '2.fq' => 'bam2fq/8.2.fq.expected', 's.fq' => 'bam2fq/8.s.fq.expected', 'i.fq' => 'bam2fq/8.i.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -i \-\-index-format 'n2i2' \-\-i1 $$opts{path}/i.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
489 <test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
490 <param name="input" value="bam2fq.004.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
491 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
492 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
493 <param name="ilumina_casava" value="-i" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
494 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
495 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
496 <conditional name="idxout_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
497 <param name="idxout_select" value="yes"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
498 <param name="write1st" value="yes"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
499 <param name="barcode_tag" value="BC"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
500 <param name="index_format" value="n2i2"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
501 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
502 <output name="forward" file="8.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
503 <output name="reverse" file="8.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
504 <output name="singletons" file="8.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
505 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
506 <output name="i1" file="8.i.fq.expected" ftype="fastqsanger" />
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
507 </test>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
508 </tests>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
509 <help><![CDATA[
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
510 This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
511 SAM or BAM file in FASTA or FASTQ format.
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
512 ]]>
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
513 </help>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
514 <expand macro="citations" />
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
515 </tool>