Mercurial > repos > iuc > samtools_fastx

annotate samtools_fastx.xml @ 5:b906586a6596 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:25:53 +0000
parents 66e23b11feae
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 3
diff changeset
1 <tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
1
a8d69aee190e 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
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
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3 <macros>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
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4 <import>macros.xml</import>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
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5 </macros>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
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6 <expand macro="requirements" />
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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7 <expand macro="stdio"/>
0
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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8 <expand macro="version_command" />
1
a8d69aee190e 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[
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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10 @ADDTHREADS@
1
a8d69aee190e 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
a8d69aee190e 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 $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'):
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720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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13 samtools sort -@ \$addthreads -n '$input' -T "\${TMPDIR:-.}" > input &&
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a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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14 #else:
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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15 ln -s '$input' input &&
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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16 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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17
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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18 #set command=str($output_fmt_cond.output_fmt_select)[:5]
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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19
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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20 samtools $command
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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21 #if str($output_fmt_cond.output_fmt_select).startswith('fastq'):
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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22 #if str($output_fmt_cond.default_quality) != '':
a8d69aee190e 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
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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24 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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25 $output_fmt_cond.output_quality
a8d69aee190e 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
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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27 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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28 $copy_tags
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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29 #if str($copy_arb_tags) != '':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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30 -T '$copy_arb_tags'
a8d69aee190e 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
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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32 $read_numbering
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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33 #if 'r0' in str($outputs):
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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34 -0 nonspecific.$output_fmt_cond.output_fmt_select
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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35 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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36 #if 'r1' in str($outputs):
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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37 -1 forward.$output_fmt_cond.output_fmt_select
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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38 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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39 #if 'r2' in str($outputs):
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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40 -2 reverse.$output_fmt_cond.output_fmt_select
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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41 #end if
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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42 #set $filter = $inclusive_filter
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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43 @FLAGS@
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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44 -f $flags
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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45 #set $filter = $exclusive_filter
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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46 @FLAGS@
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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47 -F $flags
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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48 #set $filter = $exclusive_filter_all
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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49 @FLAGS@
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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50 -G $flags
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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51 #if 's' in str($outputs):
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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52 -s singletons.$output_fmt_cond.output_fmt_select
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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53 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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54 #if str($idxout_cond.idxout_select) == 'yes':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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55 #if str($idxout_cond.write1st) == 'yes':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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56 --i1 i1.$output_fmt_cond.output_fmt_select
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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57 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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58 #if str($idxout_cond.write2nd) == 'yes':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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59 --i2 i2.$output_fmt_cond.output_fmt_select
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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60 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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61 #if str($idxout_cond.index_format) != '':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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62 --index-format $idxout_cond.index_format
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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63 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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64 #if str($idxout_cond.barcode_tag) != '':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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65 --barcode-tag $idxout_cond.barcode_tag
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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66 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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67 #if str($idxout_cond.quality_tag) != '':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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68 --quality-tag $idxout_cond.quality_tag
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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69 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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70 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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71
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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72 input
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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73
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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74 #if str($outputs)=='None' or 'other' in str($outputs):
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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75 ## since currently stdout in not zipped (samtools doesn't know about the extension)
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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76 #if str($output_fmt_cond.output_fmt_select).endswith('.gz'):
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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77 | gzip -
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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78 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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79 > output.$output_fmt_cond.output_fmt_select
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80 && ln -s output.$output_fmt_cond.output_fmt_select output
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81 #else
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82 ## otherwise the remaining sequences would show up in the datasets info box
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83 > /dev/null
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84 #end if
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85 #if 'r0' in str($outputs):
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86 && ln -s nonspecific.$output_fmt_cond.output_fmt_select nonspecific
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87 #end if
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88 #if 'r1' in str($outputs):
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89 && ln -s forward.$output_fmt_cond.output_fmt_select forward
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90 #end if
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91 #if 'r2' in str($outputs):
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92 && ln -s reverse.$output_fmt_cond.output_fmt_select reverse
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93 #end if
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94 #if 's' in str($outputs):
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95 && ln -s singletons.$output_fmt_cond.output_fmt_select singletons
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96 #end if
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97 #if str($idxout_cond.idxout_select) == 'yes':
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98 #if str($idxout_cond.write1st) == 'yes':
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99 && ln -s i1.$output_fmt_cond.output_fmt_select i1
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100 #end if
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101 #if str($idxout_cond.write2nd) == 'yes':
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102 && ln -s i2.$output_fmt_cond.output_fmt_select i2
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103 #end if
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104 #end if
0
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105 ]]>
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106 </command>
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107 <inputs>
1
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108 <param name="input" type="data" format="sam,bam,cram" label="BAM or SAM file to convert" />
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109 <conditional name="output_fmt_cond">
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110 <param name="output_fmt_select" type="select" label="Output format">
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111 <option value="fasta" selected="True">FASTA</option>
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112 <option value="fastqsanger">FASTQ</option>
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113 <option value="fasta.gz">compressed FASTA</option>
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114 <option value="fastqsanger.gz">compressed FASTQ</option>
0
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115 </param>
1
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116 <when value="fastqsanger">
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117 <param name="default_quality" argument="-v" type="integer" optional="True" label="Default quality if none is given" />
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118 <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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119 <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
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120 </when>
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121 <when value="fasta" />
1
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122 <when value="fastqsanger.gz">
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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)" />
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126 </when>
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127 <when value="fasta.gz" />
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128 </conditional>
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129 <param name="outputs" type="select" multiple="true" label="outputs">
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130 <option value="other" selected="true">others</option>
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131 <option value="r1">READ1</option>
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132 <option value="r2">READ2</option>
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133 <option value="s">singletons</option>
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134 <option value="r0">unspecific</option>
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135 <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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136 </param>
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137 <param name="copy_tags" argument="-t" type="boolean" truevalue="-t" falsevalue="" label="Copy RG/BC/QT tags to output header" />
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138 <param name="copy_arb_tags" argument="-T" type="text" optional="true" label="copy arbitrary tags to the FASTA header line" />
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139 <param name="read_numbering" type="select" label="Omit or append read numbers">
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140 <option value="" selected="True">no</option>
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141 <option value="-n">Do not append /1 and /2 to read names</option>
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142 <option value="-N">always append /1 and /2 to read name</option>
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143 </param>
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144 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
2
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145 <expand macro="flag_options"/>
1
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146 </param>
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147 <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
2
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148 <expand macro="flag_options" s256="true" s2048="true"/>
1
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149 </param>
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150 <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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151 <expand macro="flag_options" />
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152 </param>
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153
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154 <conditional name="idxout_cond">
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155 <param name="idxout_select" type="select" label="Write index read files">
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156 <option value="no" selected="True">No</option>
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157 <option value="yes">Yes (beta: feedback welcome)</option>
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158 </param>
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159 <when value="no" />
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160 <when value="yes">
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161 <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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162 <param name="write2nd" argument="--i2" type="boolean" truevalue="yes" falsevalue="no" checked='true' label="write second index reads to extra data set" />
4
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163 <param argument="--index-format" type="text" label="Index format: How to parse barcode and quality tags">
1
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164 <help>
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165 The index-format string describes how to parse the barcode and quality tags, for example:
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166 i14i8 the first 14 characters are index 1, the next 8 characters are index 2
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167 n8i14 ignore the first 8 characters, and use the next 14 characters for index 1
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168 If the tag contains a separator, then the numeric part can be replaced with '*' to mean
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169 'read until the separator or end of tag', for example:
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170 n*i* ignore the left part of the tag until the separator, then use the second part
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171 of the tag as index 1
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172 </help>
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173 </param>
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174 <param argument="--barcode-tag" type="text" optional="True" label="Barcode tag [default: BC]"/>
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175 <param argument="--quality-tag" type="text" optional="True" label="Quality tag [default: QT]"/>
1
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176 </when>
0
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177 </conditional>
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178 </inputs>
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179 <outputs>
1
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180 <data name="nonspecific" format="fasta" from_work_dir="nonspecific" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (nonspecific)">
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181 <filter>'r0' in str(outputs)</filter>
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182 <actions>
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183 <action type="format">
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184 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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185 </action>
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186 </actions>
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187 </data>
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188 <data name="forward" format="fasta" from_work_dir="forward" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (READ1)">
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189 <filter>'r1' in str(outputs)</filter>
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190 <actions>
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191 <action type="format">
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192 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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193 </action>
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194 </actions>
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195 </data>
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196 <data name="reverse" format="fasta" from_work_dir="reverse" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (READ2)">
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197 <filter>'r2' in str(outputs)</filter>
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198 <actions>
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199 <action type="format">
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200 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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201 </action>
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202 </actions>
0
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203 </data>
1
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204 <data name="singletons" format="fasta" from_work_dir="singletons" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (singletons)">
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205 <filter>'s' in str(outputs)</filter>
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206 <actions>
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207 <action type="format">
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208 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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209 </action>
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210 </actions>
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211 </data>
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212 <data name="output" format="fasta" from_work_dir="output" label="${on_string} converted to ${output_fmt_cond.output_fmt_select}">
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213 <filter>str(outputs)=='None' or 'other' in str(outputs)</filter>
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214 <actions>
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215 <action type="format">
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216 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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217 </action>
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218 </actions>
0
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219 </data>
1
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220 <data name="i1" format="fasta" from_work_dir="i1" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (1st index)">
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221 <filter>idxout_cond['idxout_select']=='yes' and idxout_cond['write1st']</filter>
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222 <actions>
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223 <action type="format">
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224 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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225 </action>
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226 </actions>
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227 </data>
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228 <data name="i2" format="fasta" from_work_dir="i2" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (2nd index)">
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229 <filter>idxout_cond['idxout_select']=='yes' and idxout_cond['write2nd']</filter>
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230 <actions>
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231 <action type="format">
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232 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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233 </action>
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234 </actions>
0
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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235 </data>
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236 </outputs>
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237 <tests>
1
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238 <!-- tests from original Galaxy tool -->
4
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239 <test expect_num_outputs="1">
0
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240 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
1
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241 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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242 <param name="output_fmt_select" value="fasta" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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243 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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244 <param name="outputs" value="other" />
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245 <output name="output" file="samtools_fastx-out1.fasta" ftype="fasta" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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246 </test>
4
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247 <test expect_num_outputs="3">
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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248 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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249 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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250 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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251 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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252 <param name="outputs" value="r0,r1,r2" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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253 <output name="nonspecific" file="samtools_fastx-out2-1.fastq" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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254 <output name="forward" file="samtools_fastx-out2-2.fastq" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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255 <output name="reverse" file="samtools_fastx-out2-3.fastq" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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256 </test>
4
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257 <test expect_num_outputs="3">
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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258 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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259 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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260 <param name="output_fmt_select" value="fasta" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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261 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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262 <param name="outputs" value="r0,r1,r2" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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263 <output name="nonspecific" file="samtools_fastx-out3-1.fasta" ftype="fasta" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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264 <output name="forward" file="samtools_fastx-out3-2.fasta" ftype="fasta" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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265 <output name="reverse" file="samtools_fastx-out3-3.fasta" ftype="fasta" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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266 </test>
2
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267 <!-- tests from original Galaxy tool with gz output. for some reason gzip (which is used
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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268 for compressing stdout does not give exactly the same file contents .. the other
1
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269 compressed files seem to)-->
4
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270 <test expect_num_outputs="1">
1
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271 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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272 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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273 <param name="output_fmt_select" value="fasta.gz" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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274 </conditional>
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275 <param name="outputs" value="other" />
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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276 <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" decompress="true"/>
0
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277 </test>
4
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278 <test expect_num_outputs="3">
0
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279 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
1
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280 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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281 <param name="output_fmt_select" value="fastqsanger.gz" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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282 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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283 <param name="outputs" value="r0,r1,r2" />
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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284 <output name="nonspecific" file="samtools_fastx-out2-1.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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285 <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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286 <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
0
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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287 </test>
4
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288 <test expect_num_outputs="3">
0
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289 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
1
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diff changeset
290 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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291 <param name="output_fmt_select" value="fasta.gz" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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292 </conditional>
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293 <param name="outputs" value="r0,r1,r2" />
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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294 <output name="nonspecific" file="samtools_fastx-out3-1.fasta.gz" ftype="fasta.gz" decompress="true" />
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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295 <output name="forward" file="samtools_fastx-out3-2.fasta.gz" ftype="fasta.gz" decompress="true" />
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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diff changeset
296 <output name="reverse" file="samtools_fastx-out3-3.fasta.gz" ftype="fasta.gz" decompress="true" />
1
a8d69aee190e 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
297 </test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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298 <!-- tests from: https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2313-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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299 <!--# basic 2 output test without singleton tracking-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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300 <!--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");-->
4
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
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301 <test expect_num_outputs="3">
1
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302 <param name="input" value="bam2fq.001.sam" ftype="sam" />
a8d69aee190e 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
303 <conditional name="output_fmt_cond">
a8d69aee190e 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
304 <param name="output_fmt_select" value="fastqsanger" />
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305 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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306 <param name="outputs" value="r1,r2,other" />
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307 <output name="forward" file="1.1.fq.expected" ftype="fastqsanger" />
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308 <output name="reverse" file="1.2.fq.expected" ftype="fastqsanger" />
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309 <output name="output" file="1.stdout.expected" ftype="fastqsanger" />
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310 </test>
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311 <!--# basic 2 output test with singleton tracking but no singleton-->
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312 <!--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 $$opts{path}/dat/bam2fq.001.sam");-->
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313 <test expect_num_outputs="4">
1
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314 <param name="input" value="bam2fq.001.sam" ftype="sam" />
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315 <conditional name="output_fmt_cond">
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316 <param name="output_fmt_select" value="fastqsanger" />
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317 </conditional>
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318 <param name="outputs" value="r1,r2,s,other" />
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319 <output name="forward" file="2.1.fq.expected" ftype="fastqsanger" />
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320 <output name="reverse" file="2.2.fq.expected" ftype="fastqsanger" />
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321 <output name="singletons" file="2.s.fq.expected" ftype="fastqsanger" />
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322 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
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323 </test>
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324 <!--# basic 2 output test with singleton tracking with a singleton in the middle-->
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325 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/3.1.fq.expected', '2.fq' => 'bam2fq/3.2.fq.expected', 's.fq' => 'bam2fq/3.s.fq.expected'}, cmd=>"$$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");-->
4
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326 <test expect_num_outputs="4">
1
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327 <param name="input" value="bam2fq.002.sam" ftype="sam" />
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328 <conditional name="output_fmt_cond">
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329 <param name="output_fmt_select" value="fastqsanger" />
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330 </conditional>
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331 <param name="outputs" value="r1,r2,s,other" />
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332 <output name="forward" file="3.1.fq.expected" ftype="fastqsanger" />
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333 <output name="reverse" file="3.2.fq.expected" ftype="fastqsanger" />
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334 <output name="singletons" file="3.s.fq.expected" ftype="fastqsanger" />
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335 <output name="output" file="3.stdout.expected" ftype="fastqsanger" />
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336 </test>
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337 <!--# basic 2 output test with singleton tracking with a singleton as last read-->
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338 <!--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 $$opts{path}/dat/bam2fq.003.sam");-->
4
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339 <test expect_num_outputs="4">
1
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340 <param name="input" value="bam2fq.003.sam" ftype="sam" />
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341 <conditional name="output_fmt_cond">
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342 <param name="output_fmt_select" value="fastqsanger" />
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343 </conditional>
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344 <param name="outputs" value="r1,r2,s,other" />
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345 <output name="forward" file="4.1.fq.expected" ftype="fastqsanger" />
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346 <output name="reverse" file="4.2.fq.expected" ftype="fastqsanger" />
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347 <output name="singletons" file="4.s.fq.expected" ftype="fastqsanger" />
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348 <output name="output" file="4.stdout.expected" ftype="fastqsanger" />
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349 </test>
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350 <!--# tag output test with singleton tracking with a singleton as last read-->
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351 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$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");-->
4
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352 <test expect_num_outputs="5">
1
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353 <param name="input" value="bam2fq.004.sam" ftype="sam" />
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354 <conditional name="output_fmt_cond">
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355 <param name="output_fmt_select" value="fastqsanger" />
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356 </conditional>
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357 <param name="outputs" value="r1,r2,s,other" />
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358 <conditional name="idxout_cond">
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359 <param name="idxout_select" value="yes"/>
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360 <param name="write1st" value="true"/>
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361 <param name="write2nd" value="false"/>
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362 <param name="barcode_tag" value="BC"/>
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363 <param name="index_format" value="n2i2"/>
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364 </conditional>
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365 <output name="forward" file="4.1.fq.expected" ftype="fastqsanger" />
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366 <output name="reverse" file="4.2.fq.expected" ftype="fastqsanger" />
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367 <output name="singletons" file="4.s.fq.expected" ftype="fastqsanger" />
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368 <output name="output" file="4.stdout.expected" ftype="fastqsanger" />
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369 <output name="i1" file="bc.fq.expected" ftype="fastqsanger" />
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370 </test>
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371 <!--# test -O flag with no OQ tags-->
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372 <!--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");-->
4
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373 <test expect_num_outputs="5">
1
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374 <param name="input" value="bam2fq.010.sam" ftype="sam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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375 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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376 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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377 <param name="output_quality" value="-O" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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378 </conditional>
a8d69aee190e 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="outputs" value="r1,r2,s,other" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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380 <conditional name="idxout_cond">
a8d69aee190e 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="idxout_select" value="yes"/>
4
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382 <param name="write1st" value="true"/>
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
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383 <param name="write2nd" value="false"/>
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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384 <param name="barcode_tag" value="BC"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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385 <param name="index_format" value="n2i2"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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386 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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387 <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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388 <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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389 <output name="singletons" file="10.s.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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390 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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391 <output name="i1" file="bc10.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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392 </test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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393 <!--# test -O flag with OQ tags-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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394 <!--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");-->
4
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
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395 <test expect_num_outputs="5">
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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396 <param name="input" value="bam2fq.010.sam" ftype="sam" />
a8d69aee190e 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
397 <conditional name="output_fmt_cond">
a8d69aee190e 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
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398 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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399 <param name="output_quality" value="-O" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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400 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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401 <param name="outputs" value="r1,r2,s,other" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
402 <conditional name="idxout_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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403 <param name="idxout_select" value="yes"/>
4
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
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parents: 3
diff changeset
404 <param name="write1st" value="true"/>
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
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405 <param name="write2nd" value="false"/>
1
a8d69aee190e 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
406 <param name="barcode_tag" value="BC"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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407 <param name="index_format" value="n2i2"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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408 </conditional>
a8d69aee190e 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 <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" />
a8d69aee190e 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 <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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411 <output name="singletons" file="10.s.fq.expected" ftype="fastqsanger" />
a8d69aee190e 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
412 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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413 <output name="i1" file="bc10.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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414 </test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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415 <!--# tag output test with separators and -N flag-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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416 <!--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");-->
4
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
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diff changeset
417 <test expect_num_outputs="5">
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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418 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a8d69aee190e 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
419 <conditional name="output_fmt_cond">
a8d69aee190e 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
420 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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421 </conditional>
a8d69aee190e 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
422 <param name="outputs" value="r1,r2,s,other" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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423 <param name="read_numbering" value="-N"/>
a8d69aee190e 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
424 <conditional name="idxout_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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425 <param name="idxout_select" value="yes"/>
4
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
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parents: 3
diff changeset
426 <param name="write1st" value="true"/>
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
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427 <param name="write2nd" value="false"/>
1
a8d69aee190e 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="barcode_tag" value="BC"/>
a8d69aee190e 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="index_format" value="n*i*"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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430 </conditional>
a8d69aee190e 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 <output name="forward" file="5.1.fq.expected" ftype="fastqsanger" />
a8d69aee190e 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
432 <output name="reverse" file="5.2.fq.expected" ftype="fastqsanger" />
a8d69aee190e 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="singletons" file="5.s.fq.expected" ftype="fastqsanger" />
a8d69aee190e 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="output" file="2.stdout.expected" ftype="fastqsanger" />
a8d69aee190e 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
435 <output name="i1" file="bc_split.fq.expected" ftype="fastqsanger" />
a8d69aee190e 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 </test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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437 <!--# -t flag-->
a8d69aee190e 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_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");-->
4
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
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diff changeset
439 <test expect_num_outputs="4">
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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440 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
441 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
442 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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443 </conditional>
a8d69aee190e 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="outputs" value="r1,r2,s,other" />
a8d69aee190e 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
445 <param name="copy_tags" value="-t" />
a8d69aee190e 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
446 <param name="read_numbering" value="-N"/>
a8d69aee190e 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 <output name="forward" file="6.1.fq.expected" ftype="fastqsanger" />
a8d69aee190e 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 <output name="reverse" file="6.2.fq.expected" ftype="fastqsanger" />
a8d69aee190e 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="singletons" file="6.s.fq.expected" ftype="fastqsanger" />
a8d69aee190e 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="output" file="2.stdout.expected" ftype="fastqsanger" />
a8d69aee190e 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 </test>
a8d69aee190e 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 <!--# -T flag-->
a8d69aee190e 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_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");-->
4
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 3
diff changeset
454 <test expect_num_outputs="4">
1
a8d69aee190e 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 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a8d69aee190e 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 <conditional name="output_fmt_cond">
a8d69aee190e 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="output_fmt_select" value="fastqsanger" />
a8d69aee190e 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>
a8d69aee190e 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="outputs" value="r1,r2,s,other" />
a8d69aee190e 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 <param name="copy_tags" value="-t" />
a8d69aee190e 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="copy_arb_tags" value="MD,ia" />
a8d69aee190e 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="read_numbering" value="-N"/>
a8d69aee190e 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 <output name="forward" file="7.1.fq.expected" ftype="fastqsanger" />
a8d69aee190e 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 <output name="reverse" file="7.2.fq.expected" ftype="fastqsanger" />
a8d69aee190e 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="singletons" file="7.s.fq.expected" ftype="fastqsanger" />
a8d69aee190e 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="output" file="2.stdout.expected" ftype="fastqsanger" />
a8d69aee190e 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 </test>
a8d69aee190e 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 <!--# -i flag with no index-->
a8d69aee190e 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_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");-->
4
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 3
diff changeset
470 <test expect_num_outputs="6">
1
a8d69aee190e 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 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a8d69aee190e 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 <conditional name="output_fmt_cond">
a8d69aee190e 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="output_fmt_select" value="fastqsanger" />
a8d69aee190e 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 <param name="ilumina_casava" value="-i" />
a8d69aee190e 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 </conditional>
a8d69aee190e 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="outputs" value="r1,r2,s,other" />
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
477 <conditional name="idxout_cond">
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
478 <param name="idxout_select" value="yes"/>
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
479 <param name="index_format" value="n2i2"/>
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
480 </conditional>
1
a8d69aee190e 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="copy_tags" value="-t" />
a8d69aee190e 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 <param name="copy_arb_tags" value="MD,ia" />
a8d69aee190e 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 <param name="read_numbering" value="-N"/>
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
484 <output name="forward" file="11.1.fq.expected" ftype="fastqsanger" />
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
485 <output name="reverse" file="11.2.fq.expected" ftype="fastqsanger" />
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
486 <output name="singletons" file="11.s.fq.expected" ftype="fastqsanger" />
1
a8d69aee190e 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 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
4
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 3
diff changeset
488 <output name="i1" file="11.i.fq.expected" ftype="fastqsanger" />
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 3
diff changeset
489 <output name="i2" file="11.i2.fq.expected" ftype="fastqsanger" />
1
a8d69aee190e 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 </test>
a8d69aee190e 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 <!--# -i flag with index-->
a8d69aee190e 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 <!--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");-->
4
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 3
diff changeset
493 <test expect_num_outputs="6">
1
a8d69aee190e 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 <param name="input" value="bam2fq.004.sam" ftype="sam" />
a8d69aee190e 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 <conditional name="output_fmt_cond">
a8d69aee190e 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 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e 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="ilumina_casava" value="-i" />
a8d69aee190e 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 </conditional>
a8d69aee190e 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="outputs" value="r1,r2,s,other" />
a8d69aee190e 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 <conditional name="idxout_cond">
a8d69aee190e 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 <param name="idxout_select" value="yes"/>
4
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 3
diff changeset
502 <param name="write1st" value="true"/>
1
a8d69aee190e 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 <param name="barcode_tag" value="BC"/>
a8d69aee190e 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 <param name="index_format" value="n2i2"/>
a8d69aee190e 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 </conditional>
a8d69aee190e 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="forward" file="8.1.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
507 <output name="reverse" file="8.2.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
508 <output name="singletons" file="8.s.fq.expected" ftype="fastqsanger" />
a8d69aee190e 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 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a8d69aee190e 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 <output name="i1" file="8.i.fq.expected" ftype="fastqsanger" />
4
66e23b11feae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 3
diff changeset
511 <output name="i2" file="8.i2.fq.expected" ftype="fastqsanger" />
0
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
parents:
diff changeset
512 </test>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
parents:
diff changeset
513 </tests>
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
514 <help><![CDATA[
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
515 This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
516 SAM or BAM file in FASTA or FASTQ format.
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
517 ]]>
0
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
parents:
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518 </help>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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519 <expand macro="citations" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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520 </tool>