Mercurial > repos > iuc > samtools_fastx
annotate samtools_fastx.xml @ 7:491037bfc0d2 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_fastx commit 19dd8b645a77899ff98d139d79de824a23f416bb
| author | iuc |
|---|---|
| date | Wed, 12 Nov 2025 13:02:03 +0000 |
| parents | 9038311ed624 |
| children |
| rev | line source |
|---|---|
|
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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3
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changeset
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1 <tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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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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changeset
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2 <description>extract FASTA or FASTQ from alignment files</description> |
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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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diff
changeset
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3 <macros> |
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a0d039fa9771
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
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a0d039fa9771
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
parents:
diff
changeset
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5 </macros> |
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a0d039fa9771
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
parents:
diff
changeset
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6 <expand macro="requirements" /> |
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1
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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changeset
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7 <expand macro="stdio"/> |
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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
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8 <expand macro="version_command" /> |
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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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changeset
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9 <command><![CDATA[ |
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2
720217c23995
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
1
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changeset
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10 @ADDTHREADS@ |
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1
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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changeset
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11 ## name sort input file if neccessary |
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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
parents:
0
diff
changeset
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12 #if not $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'): |
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2
720217c23995
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
1
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changeset
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13 samtools sort -@ \$addthreads -n '$input' -T "\${TMPDIR:-.}" > input && |
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1
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
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14 #else: |
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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
parents:
0
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changeset
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15 ln -s '$input' input && |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
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16 #end if |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
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17 |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
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18 #set command=str($output_fmt_cond.output_fmt_select)[:5] |
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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
parents:
0
diff
changeset
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19 |
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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
parents:
0
diff
changeset
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20 samtools $command |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
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21 #if str($output_fmt_cond.output_fmt_select).startswith('fastq'): |
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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
parents:
0
diff
changeset
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22 #if str($output_fmt_cond.default_quality) != '': |
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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
parents:
0
diff
changeset
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23 -v $output_fmt_cond.default_quality |
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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
parents:
0
diff
changeset
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24 #end if |
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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
parents:
0
diff
changeset
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25 $output_fmt_cond.output_quality |
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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
parents:
0
diff
changeset
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26 $output_fmt_cond.ilumina_casava |
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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
parents:
0
diff
changeset
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27 #end if |
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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
parents:
0
diff
changeset
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28 $copy_tags |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
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changeset
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29 #if str($copy_arb_tags) != '': |
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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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changeset
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30 -T '$copy_arb_tags' |
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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
parents:
0
diff
changeset
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31 #end if |
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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
parents:
0
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changeset
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32 $read_numbering |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
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33 #if 'r0' in str($outputs): |
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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
parents:
0
diff
changeset
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34 -0 nonspecific.$output_fmt_cond.output_fmt_select |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
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35 #end if |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
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36 #if 'r1' in str($outputs): |
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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
parents:
0
diff
changeset
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37 -1 forward.$output_fmt_cond.output_fmt_select |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
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38 #end if |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
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39 #if 'r2' in str($outputs): |
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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
parents:
0
diff
changeset
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40 -2 reverse.$output_fmt_cond.output_fmt_select |
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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
parents:
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diff
changeset
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41 #end if |
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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
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42 #set $filter = $inclusive_filter |
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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
parents:
1
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changeset
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43 @FLAGS@ |
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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
parents:
1
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changeset
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44 -f $flags |
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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
parents:
1
diff
changeset
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45 #set $filter = $exclusive_filter |
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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
parents:
1
diff
changeset
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46 @FLAGS@ |
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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
parents:
1
diff
changeset
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47 -F $flags |
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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
parents:
1
diff
changeset
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48 #set $filter = $exclusive_filter_all |
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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
parents:
1
diff
changeset
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49 @FLAGS@ |
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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
parents:
1
diff
changeset
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50 -G $flags |
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1
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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changeset
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51 #if 's' in str($outputs): |
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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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changeset
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52 -s singletons.$output_fmt_cond.output_fmt_select |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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changeset
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53 #end if |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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changeset
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54 #if str($idxout_cond.idxout_select) == 'yes': |
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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
parents:
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changeset
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55 #if str($idxout_cond.write1st) == 'yes': |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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changeset
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56 --i1 i1.$output_fmt_cond.output_fmt_select |
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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
parents:
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changeset
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57 #end if |
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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
parents:
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changeset
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58 #if str($idxout_cond.write2nd) == 'yes': |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
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changeset
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59 --i2 i2.$output_fmt_cond.output_fmt_select |
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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
parents:
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changeset
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60 #end if |
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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
parents:
0
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changeset
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61 #if str($idxout_cond.index_format) != '': |
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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
parents:
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changeset
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62 --index-format $idxout_cond.index_format |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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changeset
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63 #end if |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
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changeset
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64 #if str($idxout_cond.barcode_tag) != '': |
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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
parents:
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changeset
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65 --barcode-tag $idxout_cond.barcode_tag |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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changeset
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66 #end if |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
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67 #if str($idxout_cond.quality_tag) != '': |
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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
parents:
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changeset
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68 --quality-tag $idxout_cond.quality_tag |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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changeset
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69 #end if |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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70 #end if |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
71 |
|
2
720217c23995
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
1
diff
changeset
|
72 input |
|
1
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
73 |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
74 #if str($outputs)=='None' or 'other' in str($outputs): |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
75 ## since currently stdout in not zipped (samtools doesn't know about the extension) |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
76 #if str($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
parents:
1
diff
changeset
|
77 | gzip - |
|
1
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
78 #end if |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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changeset
|
79 > output.$output_fmt_cond.output_fmt_select |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
80 && ln -s output.$output_fmt_cond.output_fmt_select output |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
81 #else |
|
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
|
82 ## otherwise the remaining sequences would show up in the datasets info box |
|
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
|
83 > /dev/null |
|
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
|
84 #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
diff
changeset
|
85 #if 'r0' in str($outputs): |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
86 && ln -s nonspecific.$output_fmt_cond.output_fmt_select nonspecific |
|
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
|
87 #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
diff
changeset
|
88 #if 'r1' in str($outputs): |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
89 && ln -s forward.$output_fmt_cond.output_fmt_select forward |
|
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
|
90 #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
diff
changeset
|
91 #if 'r2' in str($outputs): |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
92 && ln -s reverse.$output_fmt_cond.output_fmt_select reverse |
|
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
|
93 #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
diff
changeset
|
94 #if 's' in str($outputs): |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
95 && ln -s singletons.$output_fmt_cond.output_fmt_select singletons |
|
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
|
96 #end if |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
97 #if str($idxout_cond.idxout_select) == 'yes': |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
98 #if str($idxout_cond.write1st) == 'yes': |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
99 && ln -s i1.$output_fmt_cond.output_fmt_select i1 |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
100 #end if |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
101 #if str($idxout_cond.write2nd) == 'yes': |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
0
diff
changeset
|
102 && ln -s i2.$output_fmt_cond.output_fmt_select i2 |
|
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
|
103 #end if |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
104 #end if |
|
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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changeset
|
105 ]]> |
|
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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diff
changeset
|
106 </command> |
|
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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changeset
|
107 <inputs> |
|
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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108 <param name="input" type="data" format="sam,bam,cram" label="BAM or SAM file to convert" /> |
|
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
|
109 <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:
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diff
changeset
|
110 <param name="output_fmt_select" type="select" label="Output format"> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
111 <option value="fasta" selected="True">FASTA</option> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
112 <option value="fastqsanger">FASTQ</option> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
113 <option value="fasta.gz">compressed FASTA</option> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
114 <option value="fastqsanger.gz">compressed FASTQ</option> |
|
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
|
115 </param> |
|
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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changeset
|
116 <when value="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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changeset
|
117 <param name="default_quality" argument="-v" type="integer" optional="True" label="Default quality if none is given" /> |
|
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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|
118 <param name="output_quality" argument="-O" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Output quality in the OQ tag if available" /> |
|
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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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
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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diff
changeset
|
120 </when> |
|
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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|
121 <when value="fasta" /> |
|
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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changeset
|
122 <when value="fastqsanger.gz"> |
|
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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changeset
|
123 <param name="default_quality" argument="-v" type="integer" optional="True" label="Default quality if none is given" /> |
|
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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|
124 <param name="output_quality" argument="-O" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Output quality in the OQ tag if available" /> |
|
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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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)" /> |
|
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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changeset
|
126 </when> |
|
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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|
127 <when value="fasta.gz" /> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
128 </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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129 <param name="outputs" type="select" multiple="true" label="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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130 <option value="other" selected="true">others</option> |
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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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131 <option value="r1">READ1</option> |
|
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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132 <option value="r2">READ2</option> |
|
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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133 <option value="s">singletons</option> |
|
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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134 <option value="r0">unspecific</option> |
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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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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> |
|
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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|
136 </param> |
|
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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137 <param name="copy_tags" argument="-t" type="boolean" truevalue="-t" falsevalue="" label="Copy RG/BC/QT tags to output header" /> |
|
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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138 <param name="copy_arb_tags" argument="-T" type="text" optional="true" label="copy arbitrary tags to the FASTA header line" /> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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139 <param name="read_numbering" type="select" label="Omit or append read numbers"> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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140 <option value="" selected="True">no</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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141 <option value="-n">Do not append /1 and /2 to read names</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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142 <option value="-N">always append /1 and /2 to read name</option> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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143 </param> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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144 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set"> |
|
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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145 <expand macro="flag_options"/> |
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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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146 </param> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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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"> |
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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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148 <expand macro="flag_options" s256="true" s2048="true"/> |
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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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149 </param> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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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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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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151 <expand macro="flag_options" /> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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152 </param> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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153 |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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154 <conditional name="idxout_cond"> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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155 <param name="idxout_select" type="select" label="Write index read files"> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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156 <option value="no" selected="True">No</option> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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157 <option value="yes">Yes (beta: feedback welcome)</option> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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158 </param> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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159 <when value="no" /> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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160 <when value="yes"> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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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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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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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" /> |
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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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163 <param argument="--index-format" type="text" label="Index format: How to parse barcode and quality tags"> |
|
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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164 <help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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165 The index-format string describes how to parse the barcode and quality tags, for example: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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166 i14i8 the first 14 characters are index 1, the next 8 characters are index 2 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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167 n8i14 ignore the first 8 characters, and use the next 14 characters for index 1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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169 'read until the separator or end of tag', for example: |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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171 of the tag as index 1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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172 </help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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173 </param> |
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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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174 <param argument="--barcode-tag" type="text" optional="True" label="Barcode tag [default: BC]"/> |
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66e23b11feae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
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175 <param argument="--quality-tag" type="text" optional="True" label="Quality tag [default: QT]"/> |
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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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176 </when> |
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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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177 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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178 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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179 <outputs> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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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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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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181 <filter>'r0' in str(outputs)</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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182 <actions> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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183 <action type="format"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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184 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" /> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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185 </action> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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186 </actions> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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187 </data> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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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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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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189 <filter>'r1' in str(outputs)</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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190 <actions> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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191 <action type="format"> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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192 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" /> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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193 </action> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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194 </actions> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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195 </data> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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197 <filter>'r2' in str(outputs)</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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198 <actions> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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199 <action type="format"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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200 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" /> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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201 </action> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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202 </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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203 </data> |
|
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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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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205 <filter>'s' in str(outputs)</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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206 <actions> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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207 <action type="format"> |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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208 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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209 </action> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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210 </actions> |
|
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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211 </data> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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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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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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213 <filter>str(outputs)=='None' or 'other' in str(outputs)</filter> |
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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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214 <actions> |
|
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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changeset
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215 <action type="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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216 <option type="from_param" name="output_fmt_cond" param_attribute="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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217 </action> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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218 </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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219 </data> |
|
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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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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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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221 <filter>idxout_cond['idxout_select']=='yes' and idxout_cond['write1st']</filter> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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222 <actions> |
|
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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223 <action type="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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224 <option type="from_param" name="output_fmt_cond" param_attribute="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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225 </action> |
|
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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226 </actions> |
|
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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227 </data> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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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)"> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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229 <filter>idxout_cond['idxout_select']=='yes' and idxout_cond['write2nd']</filter> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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230 <actions> |
|
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
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231 <action type="format"> |
|
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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232 <option type="from_param" name="output_fmt_cond" param_attribute="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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233 </action> |
|
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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234 </actions> |
|
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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235 </data> |
|
a0d039fa9771
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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236 </outputs> |
|
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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237 <tests> |
|
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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238 <!-- tests from original Galaxy tool --> |
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6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
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239 <!-- 1 --> |
|
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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240 <test expect_num_outputs="1"> |
|
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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241 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" /> |
|
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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changeset
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242 <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
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243 <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
iuc
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244 </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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245 <param name="outputs" value="other" /> |
|
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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246 <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
iuc
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|
247 </test> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
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248 <!-- 2 --> |
|
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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249 <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
iuc
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diff
changeset
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250 <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
iuc
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changeset
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251 <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:
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|
252 <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
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253 </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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254 <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
iuc
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changeset
|
255 <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
iuc
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diff
changeset
|
256 <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
iuc
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changeset
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257 <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
iuc
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258 </test> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
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259 <!-- 3 --> |
|
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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260 <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
iuc
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|
261 <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
iuc
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changeset
|
262 <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:
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changeset
|
263 <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
iuc
parents:
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264 </conditional> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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|
265 <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
iuc
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changeset
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266 <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
iuc
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changeset
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267 <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
iuc
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268 <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
iuc
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269 </test> |
|
2
720217c23995
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
1
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|
270 <!-- 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"
iuc
parents:
1
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changeset
|
271 for compressing stdout does not give exactly the same file contents .. the other |
|
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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0
diff
changeset
|
272 compressed files seem to)--> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
273 <!-- 4 --> |
|
4
66e23b11feae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
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diff
changeset
|
274 <test expect_num_outputs="1"> |
|
1
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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changeset
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275 <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
iuc
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276 <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
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277 <param name="output_fmt_select" value="fasta.gz" /> |
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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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278 </conditional> |
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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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279 <param name="outputs" value="other" /> |
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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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diff
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280 <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" decompress="true"/> |
|
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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281 </test> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
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282 <!-- 5 --> |
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4
66e23b11feae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
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diff
changeset
|
283 <test expect_num_outputs="3"> |
|
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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changeset
|
284 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" /> |
|
1
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
285 <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:
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diff
changeset
|
286 <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
iuc
parents:
0
diff
changeset
|
287 </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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changeset
|
288 <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"
iuc
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changeset
|
289 <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"
iuc
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changeset
|
290 <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"
iuc
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diff
changeset
|
291 <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
iuc
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diff
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292 </test> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
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293 <!-- 6 --> |
|
4
66e23b11feae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
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diff
changeset
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294 <test expect_num_outputs="3"> |
|
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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changeset
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295 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" /> |
|
1
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
296 <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:
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diff
changeset
|
297 <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
iuc
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changeset
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298 </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
|
299 <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"
iuc
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changeset
|
300 <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"
iuc
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diff
changeset
|
301 <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"
iuc
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|
302 <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
iuc
parents:
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diff
changeset
|
303 </test> |
|
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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304 <!-- 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
iuc
parents:
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diff
changeset
|
305 <!--# 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
iuc
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306 <!--test_cmd($opts, out=>'bam2fq/1.stdout.expected', out_map=>{'1.fq' => 'bam2fq/1.1.fq.expected', '2.fq' => 'bam2fq/1.2.fq.expected'},cmd=>"$$opts{bin}/samtools fastq @$threads -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");--> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
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diff
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|
307 <!-- 7 --> |
|
4
66e23b11feae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
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diff
changeset
|
308 <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
iuc
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diff
changeset
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309 <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
iuc
parents:
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changeset
|
310 <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:
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diff
changeset
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311 <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
|
312 </conditional> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
313 <param name="outputs" value="r1,r2,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
|
314 <output name="forward" file="1.1.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
|
315 <output name="reverse" file="1.2.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
|
316 <output name="output" file="1.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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diff
changeset
|
317 </test> |
|
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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changeset
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318 <!--# basic 2 output test with singleton tracking but no singleton--> |
|
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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319 <!--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");--> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
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diff
changeset
|
320 <!-- 8 --> |
|
4
66e23b11feae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
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diff
changeset
|
321 <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
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changeset
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322 <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
iuc
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diff
changeset
|
323 <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:
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changeset
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324 <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
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changeset
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325 </conditional> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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changeset
|
326 <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:
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diff
changeset
|
327 <output name="forward" file="2.1.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
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328 <output name="reverse" file="2.2.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:
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diff
changeset
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329 <output name="singletons" file="2.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:
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changeset
|
330 <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:
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diff
changeset
|
331 </test> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
332 <!--# basic 2 output test with singleton tracking with a singleton in the middle--> |
|
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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changeset
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333 <!--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");--> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
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diff
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334 <!-- 9 --> |
|
4
66e23b11feae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
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diff
changeset
|
335 <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
|
336 <param name="input" value="bam2fq.002.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:
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diff
changeset
|
337 <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:
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diff
changeset
|
338 <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:
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diff
changeset
|
339 </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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changeset
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340 <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
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diff
changeset
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341 <output name="forward" file="3.1.fq.expected" ftype="fastqsanger" /> |
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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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diff
changeset
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342 <output name="reverse" file="3.2.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
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diff
changeset
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343 <output name="singletons" file="3.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:
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changeset
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344 <output name="output" file="3.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:
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changeset
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345 </test> |
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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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changeset
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346 <!--# basic 2 output test with singleton tracking with a singleton as last read--> |
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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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347 <!--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");--> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
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348 <!-- 10 --> |
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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
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349 <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
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diff
changeset
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350 <param name="input" value="bam2fq.003.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:
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diff
changeset
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351 <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:
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diff
changeset
|
352 <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:
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diff
changeset
|
353 </conditional> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
354 <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:
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diff
changeset
|
355 <output name="forward" file="4.1.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:
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diff
changeset
|
356 <output name="reverse" file="4.2.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:
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diff
changeset
|
357 <output name="singletons" file="4.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:
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diff
changeset
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358 <output name="output" file="4.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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changeset
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359 </test> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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changeset
|
360 <!--# tag output test with singleton tracking with a singleton as last read--> |
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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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changeset
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361 <!--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");--> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
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diff
changeset
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362 <!-- 11 --> |
|
4
66e23b11feae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
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diff
changeset
|
363 <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
iuc
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diff
changeset
|
364 <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
|
365 <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:
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diff
changeset
|
366 <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:
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diff
changeset
|
367 </conditional> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
368 <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:
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diff
changeset
|
369 <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:
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diff
changeset
|
370 <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:
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diff
changeset
|
371 <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
iuc
parents:
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diff
changeset
|
372 <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
iuc
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diff
changeset
|
373 <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:
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diff
changeset
|
374 <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:
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diff
changeset
|
375 </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
|
376 <output name="forward" file="4.1.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:
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diff
changeset
|
377 <output name="reverse" file="4.2.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:
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diff
changeset
|
378 <output name="singletons" file="4.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:
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diff
changeset
|
379 <output name="output" file="4.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
|
380 <output name="i1" file="bc.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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changeset
|
381 </test> |
|
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
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382 <!--# test -O flag with no OQ 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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changeset
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383 <!--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");--> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
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diff
changeset
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384 <!-- 12 --> |
|
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
|
385 <test expect_num_outputs="5"> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
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changeset
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386 <param name="input" value="bam2fq.004.sam" ftype="sam" /> |
|
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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diff
changeset
|
387 <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
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changeset
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388 <param name="output_fmt_select" value="fastqsanger" /> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
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changeset
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389 <param name="output_quality" 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:
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changeset
|
390 </conditional> |
|
a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents:
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diff
changeset
|
391 <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:
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changeset
|
392 <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
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changeset
|
393 <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:
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diff
changeset
|
394 <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
iuc
parents:
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changeset
|
395 <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
iuc
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changeset
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396 <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:
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diff
changeset
|
397 <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:
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changeset
|
398 </conditional> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
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diff
changeset
|
399 <output name="forward" file="4.1.fq.expected" ftype="fastqsanger" /> |
|
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
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diff
changeset
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400 <output name="reverse" file="4.2.fq.expected" ftype="fastqsanger" /> |
|
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
401 <output name="singletons" file="4.s.fq.expected" ftype="fastqsanger" /> |
|
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
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diff
changeset
|
402 <output name="output" file="4.stdout.expected" ftype="fastqsanger" /> |
|
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
403 <output name="i1" file="bc.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
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changeset
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404 </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
|
405 <!--# 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
iuc
parents:
0
diff
changeset
|
406 <!--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");--> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
407 <!-- 13 --> |
|
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
|
408 <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
iuc
parents:
0
diff
changeset
|
409 <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
iuc
parents:
0
diff
changeset
|
410 <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
|
411 <param name="output_fmt_select" value="fastqsanger" /> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
412 <param name="output_quality" 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
|
413 </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
|
414 <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
|
415 <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
|
416 <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
|
417 <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
iuc
parents:
3
diff
changeset
|
418 <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
iuc
parents:
0
diff
changeset
|
419 <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
|
420 <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
|
421 </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
|
422 <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
parents:
0
diff
changeset
|
423 <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
iuc
parents:
0
diff
changeset
|
424 <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
iuc
parents:
0
diff
changeset
|
425 <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
|
426 <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
iuc
parents:
0
diff
changeset
|
427 </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
|
428 <!--# 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
iuc
parents:
0
diff
changeset
|
429 <!--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");--> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
430 <!-- 14 --> |
|
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
|
431 <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
iuc
parents:
0
diff
changeset
|
432 <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
|
433 <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
|
434 <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
|
435 </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
|
436 <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
|
437 <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
|
438 <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
|
439 <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
|
440 <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
iuc
parents:
3
diff
changeset
|
441 <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
iuc
parents:
0
diff
changeset
|
442 <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
|
443 <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
iuc
parents:
0
diff
changeset
|
444 </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
|
445 <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
iuc
parents:
0
diff
changeset
|
446 <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
iuc
parents:
0
diff
changeset
|
447 <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
iuc
parents:
0
diff
changeset
|
448 <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
|
449 <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
iuc
parents:
0
diff
changeset
|
450 </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
|
451 <!--# -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
|
452 <!--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");--> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
453 <!-- 15 --> |
|
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" /> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
460 <param name="copy_tags" 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
|
461 <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
|
462 <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
|
463 <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
|
464 <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
|
465 <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
|
466 </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
|
467 <!--# -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
|
468 <!--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");--> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
469 <!-- 16 --> |
|
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="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
|
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 </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
|
475 <param name="outputs" value="r1,r2,s,other" /> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
476 <param name="copy_tags" 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
|
477 <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
|
478 <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
|
479 <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
|
480 <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
|
481 <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
|
482 <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
|
483 </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
|
484 <!--# -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
|
485 <!--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");--> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
486 <!-- 17 --> |
|
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
|
487 <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
|
488 <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
|
489 <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
|
490 <param name="output_fmt_select" value="fastqsanger" /> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
491 <param name="ilumina_casava" 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
|
492 </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
|
493 <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
|
494 <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
|
495 <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
|
496 <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
|
497 </conditional> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
498 <param name="copy_tags" 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
|
499 <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
|
500 <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
|
501 <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
|
502 <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
|
503 <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
|
504 <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
|
505 <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
|
506 <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
|
507 </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
|
508 <!--# -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
|
509 <!--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");--> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
510 <!-- 18 --> |
|
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 <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
|
512 <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
|
513 <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
|
514 <param name="output_fmt_select" value="fastqsanger" /> |
|
6
9038311ed624
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit c508c3af0f4121dcc38e0be63db00a604e997b8a
iuc
parents:
4
diff
changeset
|
515 <param name="ilumina_casava" 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
|
516 </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
|
517 <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
|
518 <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
|
519 <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
|
520 <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
|
521 <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
|
522 <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
|
523 </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
|
524 <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
|
525 <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
|
526 <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
|
527 <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
|
528 <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
|
529 <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
|
530 </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
|
531 </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
|
532 <help><![CDATA[ |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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533 This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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534 SAM or BAM file in FASTA or FASTQ format. |
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a8d69aee190e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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535 ]]> |
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a0d039fa9771
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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536 </help> |
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a0d039fa9771
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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537 <expand macro="citations" /> |
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a0d039fa9771
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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538 </tool> |